I have a similar problem with 5.5 and did not receive any helpfull responces. For the time being, I'm running the game server as root only when playing. When were done for the night, I stop the game server. This is certainly not the correct solution but it works for now.
User privleges seem to be a vary basic issue that many in the community assumes you know about if your messing with LINUX. Hence, I have not been able to find any clear documentation on the subject. Knowledge gaps like this are an inevitable side effect of being self taught. A clue on where to start and how privleges relate specificly to SME would be helpfull.