What bo said is part of the link I give here (he posted while I was writing)
Megiddo said somewhere that Garry broke some file things in a recent update. Not sure if that might be affecting you.
If itn's not Gmod directly, sounds like fadmin or another mod rewrote some of your groups.
Try removing/backing up/or if you want deleting your server gmod/data/ulib/groups.txt and users.txt files (while server is shut down of course).
Then restart server to see if the files are rebuilt, add yourself back to superadmin. Test. Restart again to see if it holds.
If that doesn't work, see
http://forums.ulyssesmod.net/index.php/topic,383.0.html (step 2 onward, but #1 never hurts)