How to compare directory/files and permissions on Windows?
Have you throught about using PowerShell to do this?
PS2 includes a cmdlet Get-ACL which enums the NFTS permissions (including owner) for a given folder/file.
You can use ICACLs.exe, Included since Vista or so to dump the permissions to a text file. Then use WinDiff or Beyond Compare, or whatever your favorite file comparison tool is, to see the differences.
Example icacls command line:
icacls C:\Folder1 /T > Folder1.txt