For me, a switch to compiz-fusion caused the problem you described. My
system is up-to-date, running with nvidia-glx-new drivers and is using a
compiz-fusion repository being updated daily.

I just switched from nvidia-glx to nvidia-glx-new on another machine
also having compiz-fusion installed. In both cases the bug did not
appear.

So I have 2 systems with same drivers and same software, one showing the
bug, one without any problems.

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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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