You can move the window by Alt-clicking anywhere on it. It's necessary on my 1024x600 netbook.

Anyway, on my Ubuntu system, I removed the top bar, and put its widgets on the bottom bar. Sure, it's crowded, but now I've got more pixels for my programs.

I haven't had any graphical problems on my Ubuntu 9.10 systems (Intel and nVidia graphics), but are you using sun-java instead of the gcj-java they include by default?

On the Intel system, for some reason, the sound only works in the intro screen with the animation, one second after the lobby window pops up, the sound stops. The odd thing is that the sound did work fine during the first game. Reboots don't solve this problem.