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I noticed a while back that the VirtualBox OS window is set to transparent in some cases when Compiz is also running (a lot of users have reported this, though it's not happening for everyone).

To remove the transparency from the VirtualBox window all you have to do is:

1. Close VirtualBox
2. Add a new shortcut to your Panel, name it "Sun VirtualBox" and under the "Command" field, paste this:
3. It didn't work right away for me, just after I have restarted my computer, so you may need to do that too.

The next time you want to start VirtualBox, use that shortcut and the window will not be transparent anymore.

The above command works for every application obviously, so if you are having issues with the transparency on some apps, simply put env XLIB_SKIP_ARGB_VISUALS=1 in front of the command that runs that application.