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.
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.