How to compare/diff ACLs on two directory trees?
This tool may be your best bet http://support.microsoft.com/kb/318754
Try to use:
icacls C:\Folder1 /save Folder1_ACL.txt /T
icacls C:\Folder2 /save Folder2_ACL.txt /T
And than put the two output files into a diff software like WinMerge or KDiff. With Windows tools you can run
fc Folder1_ACL.txt Folder2_ACL.txt
You will see the difference acl difference between the two folders.