The SELECT permission was denied on the object 'sysobjects', database 'mssqlsystemresource', schema 'sys'

This was a problem with the user having deny privileges as well; in my haste to grant permissions I basically gave the user everything. And deny was killing it. So as soon as I removed those permissions it worked.

I had the same error and SOLVED by removing the DB roles db_denydatawriter and db_denydatreader of the DB user. For that, select the appropriate DB user on logins >> properties >> user mappings >> find out DB and select it >> uncheck the mentioned Db user roles. Thats it !!

Execute this code on a good server which will provide you the complete rights for PUBLIC role. Copy the output and paste to the server with the issue. Execute. Try logging in again. It fixed our problem.

SELECT  SDP.state_desc ,
        SDP.permission_name ,
        SSU.[name] AS "Schema" ,
        SSO.[name] ,
        SSO.[type]
FROM    sys.sysobjects SSO
        INNER JOIN sys.database_permissions SDP ON SSO.id = SDP.major_id
        INNER JOIN sys.sysusers SSU ON SSO.uid = SSU.uid
ORDER BY SSU.[name] ,
        SSO.[name]

Since there are so many possibilities for what might be wrong. Here's another possibility to look at. I ran into something where I had set up my own roles on a database. (For instance, "Administrator", "Manager", "DataEntry", "Customer", each with their own kinds of limitations) The only ones who could use it were "Manager" role or above--because they were also set up as sysadmin because they were adding users to the database (and they were highly trusted). Also, the users that were being added were Windows Domain users--using their domain credentials. (Everyone with access to the database had to be on our domain, but not everyone on the domain had access to the database--and only a few of them had access to change it.)

Anyway, this working system suddenly stopped working and I was getting error messages similar to the above. What I ended up doing that solved it was to go through all the permissions for the "public" role in that database and add those permissions to all of the roles that I had created. I know that everyone is supposed to be in the "public" role even though you can't add them (or rather, you can "add" them, but they won't "stay added").

So, in "SQL Server Management Studio", I went into my application's database, in other words (my localized names are obscured within <> brackets): " (SQL Server - sa)"\Databases\\Security\Roles\Database Roles\public". Right-click on "public" and select "Properties". In the "Database Role Properties - public" dialog, select the "Securables" page. Go through the list and for each element in the list, come up with an SQL "Grant" statement to grant exactly that permission to another role. So, for instance, there is a scalar function "[dbo].[fn_diagramobjects]" on which the "public" role has "Execute" privilege. So, I added the following line:

EXEC ( 'GRANT EXECUTE ON [dbo].[fn_diagramobjects] TO [' + @RoleName + '];' ) 

Once I had done this for all the elements in the "Securables" list, I wrapped that up in a while loop on a cursor selecting through all the roles in my roles table. This explicitly granted all the permissions of the "public" role to my database roles. At that point, all my users were working again (even after I removed their "sysadmin" access--done as a temporary measure while I figured out what happened.)

I'm sure there's a better (more elegant) way to do this by doing some kind of a query on the database objects and selecting on the public role, but after about half and hour of investigating, I wasn't figuring it out, so I just did it the brute-force method. In case it helps someone else, here's my code.

CREATE PROCEDURE [dbo].[GrantAccess]
AS
DECLARE @AppRoleName AS sysname

DECLARE AppRoleCursor CURSOR LOCAL SCROLL_LOCKS FOR
    SELECT AppRoleName FROM [dbo].[RoleList];

OPEN AppRoleCursor

FETCH NEXT FROM AppRoleCursor INTO @AppRoleName
WHILE @@FETCH_STATUS = 0
BEGIN

    EXEC ( 'GRANT EXECUTE ON [dbo].[fn_diagramobjects] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT EXECUTE ON [dbo].[sp_alterdiagram] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT EXECUTE ON [dbo].[sp_creatediagram] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT EXECUTE ON [dbo].[sp_dropdiagram] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT EXECUTE ON [dbo].[sp_helpdiagramdefinition] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT EXECUTE ON [dbo].[sp_helpdiagrams] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT EXECUTE ON [dbo].[sp_renamediagram] TO [' + @AppRoleName + '];' ) 

    EXEC ( 'GRANT SELECT ON [sys].[all_columns] TO [' + @AppRoleName + '];' )
    EXEC ( 'GRANT SELECT ON [sys].[all_objects] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[all_parameters] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[all_sql_modules] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[all_views] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[allocation_units] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[assemblies] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[assembly_files] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[assembly_modules] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[assembly_references] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[assembly_types] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[asymmetric_keys] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[certificates] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[change_tracking_tables] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[check_constraints] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[column_type_usages] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[column_xml_schema_collection_usages] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[columns] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[computed_columns] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[conversation_endpoints] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[conversation_groups] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[conversation_priorities] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[crypt_properties] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[data_spaces] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[database_audit_specification_details] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[database_audit_specifications] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[database_files] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[database_permissions] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[database_principal_aliases] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[database_principals] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[database_role_members] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[default_constraints] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[destination_data_spaces] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[event_notifications] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[events] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[extended_procedures] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[extended_properties] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[filegroups] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[foreign_key_columns] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[foreign_keys] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[fulltext_catalogs] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[fulltext_index_catalog_usages] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[fulltext_index_columns] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[fulltext_index_fragments] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[fulltext_indexes] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[fulltext_stoplists] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[fulltext_stopwords] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[function_order_columns] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[identity_columns] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[index_columns] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[indexes] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[internal_tables] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[key_constraints] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[key_encryptions] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[message_type_xml_schema_collection_usages] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[module_assembly_usages] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[numbered_procedure_parameters] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[numbered_procedures] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[objects] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[parameter_type_usages] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[parameter_xml_schema_collection_usages] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[parameters] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[partition_functions] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[partition_parameters] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[partition_range_values] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[partition_schemes] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[partitions] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[plan_guides] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[procedures] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[remote_service_bindings] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[routes] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[schemas] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[service_contract_message_usages] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[service_contract_usages] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[service_contracts] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[service_message_types] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[service_queue_usages] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[service_queues] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[services] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[spatial_index_tessellations] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[spatial_indexes] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[sql_dependencies] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[sql_modules] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[stats] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[stats_columns] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[symmetric_keys] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[synonyms] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[syscolumns] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[syscomments] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[sysconstraints] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[sysdepends] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[sysfilegroups] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[sysfiles] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[sysforeignkeys] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[sysfulltextcatalogs] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[sysindexes] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[sysindexkeys] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[sysmembers] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[sysobjects] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[syspermissions] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[sysprotects] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[sysreferences] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[system_columns] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[system_objects] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[system_parameters] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[system_sql_modules] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[system_views] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[systypes] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[sysusers] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[table_types] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[tables] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[transmission_queue] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[trigger_events] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[triggers] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[type_assembly_usages] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[types] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[views] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[xml_indexes] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[xml_schema_attributes] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[xml_schema_collections] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[xml_schema_component_placements] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[xml_schema_components] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[xml_schema_elements] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[xml_schema_facets] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[xml_schema_model_groups] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[xml_schema_namespaces] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[xml_schema_types] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[xml_schema_wildcard_namespaces] TO [' + @AppRoleName + '];' ) 
    EXEC ( 'GRANT SELECT ON [sys].[xml_schema_wildcards] TO [' + @AppRoleName + '];' ) 

    FETCH NEXT FROM AppRoleCursor INTO @AppRoleName
END

CLOSE AppRoleCursor
RETURN 0

GO

Once that is in the system, I just needed to "Exec GrantAccess" to make it work. (Of course, I have a table [RoleList] which contains a "AppRoleName" field that contains the names of the database roles.

So, the mystery remains: why did all my users lose their "public" role and why could I not give it back to them? Was this part of an update to SQL Server 2008 R2? Was it because I ran another script to delete each user and add them back so to refresh their connection with the domain? Well, this solves the issue for now.

One last warning: you probably should check the "public" role on your system before running this to make sure there isn't something missing or wrong, here. It's always possible something is different about your system.

Hope this helps someone else.