This issue might not be realy a fault of IDEA but IDEA is the only app causing the problem. Maybe you know a workaround for this.
When I close the maximized-to-fullscreen main window on Ubuntu 11.10, the content under the window does not get repainted correctly. Actually it gets repainted only under the area that would be occupied by a non-maximized window (normal size). IDEA must be doing "close" operation somehow differently than other java apps, in some way that exposes a bug in graphics driver / X server / etc. I can't notice that behavior on different Swing applications nor any native applications. Additionallly, on another computer with Intel graphics, the problem does not exist.
Closing a normal-size window also works correctly.
So if some of the developers has a nvidia card with latest drivers (295.33) on ubuntu unity 3D, please check it. If not, I can live with it, but well, I don't like when things are not perfect. :)