Comment 4 for bug 579937

Unfortunately the temporary part has been already quite some time :/

Blender 2.49 still had front-buffer drawing code that poses problems for some cards and drivers.

I don't think that this will be fixed in 2.49 (or any theoretical 2.4x series bugfix release), but you should try a Blender 2.5 build.

Blender 2.5 has a different drawing approach in that everything is now drawn in backbuffer. Please try a build for Linux from graphicall.org (or create your own build if there is no prebuilt package available). If it doesn't readily work, try changing the drawing method in Blender user preferences > System