I can replicate this by holding the mouse over a maximised VMWare window (on one of two monitors), holding down control and then moving the cursor back out of the VMWare window. After releasing the control key outside the VMWare window I find that the shift and control keys no longer work at all until I either run setxkbmap or restart my X session somehow.
I've attached output of od -x /dev/input/event1 taken while this was happening. The trace is pretty opaque to me, but there's several lines of futzing around after it happens, as I had to type setxkbmap before I could terminate the od -x logging with Ctl-C.
Needless to say, this is a killer when copying/pasting out of the VMWare window, as one slovenly Ctl-c screws the system up. I used to get this happening very occasionally under Gutsy, but it seems to happen more often following my upgrade to Hardy.