I have the exact same issue on Feisty + Nvidia legacy driver + Xgl +
Compiz

If I instead run Xorg + Metacity, the issue is gone.


My workaround is CTRL+ALT+F1 to switch to a tty and do killall gksu. That 
returns the system into a responsive state and also opens the app I requested.

Otherwise, if I wait long enough (a few minutes), gksu finishes and the
app runs.

-- 
With desktop effects enabled when using gksu system gets grey and only responds 
to keyboard 
https://bugs.launchpad.net/bugs/106008
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