I discovered this bug a couple weeks back, but I keep running up against it: Try running a modern Java IDE (NetBeans or IntelliJ, specifically) on a fancy new Linux installation, such as Ubuntu 7.04. If you have Beryl or Compiz running, you'll see nothing but an empty window. Turn off eye candy and everything works -- but anything requiring your fancy 3D window manager has to go to sleep while you slice and dice code.
I suppose it's better than nothing, but I'm starting to demand quite a bit from Linux. Here's hoping someone starts selling a Tightpinkproduct soon.
Masaki Katakai proposes some possible solutions. Try them out. Let me know how things go. If nothing else, the start of that post worth a read when translated into English. That's the sort of thing that would drive me to learn Japanese if I had any ambition.