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(Get the code!)
I too have seen this bug. I recently upgraded (GUI) from gutsy to hardy.
I thought that losing the modifier keys had something to do with vmware but I might be wrong. It seems to trigger when I leave a VM and go back into the host os. (but this might be random, as other commenters have thought)
I have found two workarounds. The first one is to save all of my work and log out, then log back in. This fixes the problem for me temporarily. The other workaround is to go to the keyboard settings and change the keyboard layout, this will fix the issue (not sure if it is temporary yet)
Also, when this bug is triggered, I find it hard to open applications (terminal is a good example), which will hang and then crash.
Another odd behaviour is that the control keys work inside the vmware guests, so the keyboard events are still happening properly, its just that hardy gets broken.
For those of you having trouble saving your work, do not forget the mouse methods for cut/paste and that selecting text usually puts it in the copy/paste buffer.