Might want to change the instructions at that link, to include the bit about editing defines.lua to stop it importing the gmod users.txt.
I know that that is what caused all of our problems when setting up the official PCGAMER Magazine (UK original) server (ooo, name dropping). It kept importing and slapping the import into the middle of our custom one, thus wrecking everything and stopping it working.
Once I found out about how to stop it importing, reinstalled our custom users.txt, and have had no problems since (except for the random stopping working that you've fixed).