Ah, thats some useful insight... That said - gnome 3 and cinnamon are also gpu accelerated so I guess it would be a unity issue.

Though the problem has gotten to the point of being enough of a nuisance to prompt me to rewrite the entire X11 code seeing as I can't get any work done until this is fixed. Once thats done, I'll see if I can get it to replicate the behaviour on the new X11 implementation to see what causes this because my code seems to be very similar to numerous xlib/opengl tutorials on the internets...