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Title pretty much says it. Keyboard shortcuts are fine. But the mouse interaction, Clicking on anything but desktop icons is... not happening.

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Are you using ubuntu 12.04? Which graphics card do you have? Does it support 30-bit/32-bit colour depth? Does the monitor support 30-/32-bit colour depth? Does it happen on all programs? There's some info about 30-bit for nvidia: download.nvidia.com/XFree86/Linux-x86/295.40/README/… –  medigeek Jun 26 '12 at 4:25
12.04, Gtx250, gpu supports, monitor supports, no it doesnt happen in all, and allll righty then. –  TardisGuy Jun 26 '12 at 10:27
Could you mention which apps are in question? Try running them in a terminal, maybe there's some debug information. According to the link I mentioned above, some apps might not work. –  medigeek Jun 26 '12 at 14:53
apps in question is the gnome shell, mouse interactivity failure.<br> keyboard works. (pure guess) The mouse is redered seperately and is not interacting at the same visual layer. –  TardisGuy Jun 30 '12 at 13:48

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