I'm running processing on a 64 bit box with aptosid (xfce or fluxbox), kubuntu (kde or fluxbox) and ArchLinux (fluxbox) and I have had no such problems ( I did have a problem running opengl sketches with ruby-processing in anything other than full-screen a year or two ago but that has since been fixed).  So assume it is gnome thing, could it have anything to do with effectively restarting opengl on resizing, which was the issue with ruby processing. I have a possible fix, turn off "all" the eye candy (disable compiz) and see what happens.