Well, I think this has been going on for awhile. I notice some of the dmflags are wrong, like Players can spy on others, players can see on automap ect. I looked at the dmflags before starting the server, and when the server starts, those dmflags are set to off.. I think they are just backwards. I tried putting the dmflags in the Additional Parameters, and they work just fine.
So yea, it needs a lil fix. either that, or something in skulltag changed.