Using vfs_gpfs + nfs4 acls/metadata on the backend, if a folder has inherited permissions and you want to set different permissions on the folder and turn off inheritance, going into the windows advanced security dialog, clicking disable inheritance -> disable only for these objects -> then clicking apply and backing out of all the dialogs and going back in you'll see that the folder still has inheritance enabled.
The only way to disable inheritance is to click disable inheritance, delete some acl, then click apply back all the way out, then go back in and you'll see inheritance is disabled. Then you re-add the acl you deleted without inheritance. This works but can sometimes take a long time since there may be many sub-folders with files on the acl that you deleted, which will then drop the acl you deleted and then they'll have to be re-added.
See the discussion in bug 13528. Marking this one as as duplicate of ot.
*** This bug has been marked as a duplicate of bug 13528 ***