Not entirely adding more to what JamminR said, but I did personally know a friend of mine who ran garry's mod servers, and his server did the same thing. Just wouldn't save in the user.txt file for some reason. I tested it thoroughly, removed all the addons, redownloaded ulx/ulib from SVN (at the time google code was cool, and everyone used it), and deleted ulx/ulib folders in the DATA folder. Still issues..
I found out one day that randomly one of his groups used a non-english character, which kinda was the cause for the issue. Strange enough, Garry's Mod/ulx still understood the non-english character, but it just didn't like saving it correctly within the group.txt or user.txt file. So my suggestion to you is if any of your groups have strange character letters in them that are not a-z, A-Z, 0-9 I would remove those character letters, and use only US-Keyboard English characters.