There is a workaround for Mathematica 6 blank windows problem. Open Option Inspector and set option WindowFrame (in Notebook Options -> Window Properties) to ThinFrame. This completely resolves the issue on my system (Slackware 12 with GNOME 2.18, compiz 0.5.2, and NVIDIA card with 100.14.09 driver). Blank windows appear momentarily when Mathematica starts, but disappear immediately.
There is a workaround for Mathematica 6 blank windows problem. Open Option Inspector and set option WindowFrame (in Notebook Options -> Window Properties) to ThinFrame. This completely resolves the issue on my system (Slackware 12 with GNOME 2.18, compiz 0.5.2, and NVIDIA card with 100.14.09 driver). Blank windows appear momentarily when Mathematica starts, but disappear immediately.
Hope this helps.