Disabling startup items that run despite being unchecked on the "login items" list

The checkboxes are not for disabling the application launch, but if checked, the application gets hidden as if you were pressing CMD+H. To disable it, select it in the list and click on the Minus-button beneath that list. By that you remove them. You can't just disable them with OS X tools.

To see a summary of all LaunchAgents and LaunchDaemons you can use a software like Lingon or you can have a look at /Library/LaunchDaemons, /Library/LaunchAgents, /System/Library/LaunchAgents, and /System/Library/LaunchDaemons as well as ~/Library/LaunchDaemons, ~/Library/LaunchAgents, ~/Library/StartupItems, and /Library/StartupItems.

All login items are can be found under System Preferences → Users & Groups → User → Login Items which you have correctly noticed.

• If you want to disable a startup item you have to remove it.
• The checkboxes are merely for hiding.
• Note: Some applications need their auto-login option to be disabled in their applications' preferences.