GameServer offline, check gamed folder, and gs proccess
It's been ages since I've touched the source files. So I can't really remember most of the codes now. However, I do remember clearly the settings are not tied to the GUI. It is tied to a file. Also, as for your other errors, it could be caused by a lot of things. Check this out java - Getting a HeadlessException: No X11 DISPLAY variable was set - Stack Overflow
You actually just needed to edit the batch to call GameServerNoUI for it to work on Linux. You didn't have to edit / remove anything. As for updating to Java 7, I would love to do that myself. But it's based on the Slick / LWJGL library. You would need to obtain the source for that and update that instead.