It's a little tough to describe the issue, but it goes something like this: There are times when my system may be crushed (lots of i/o) and I try to drag a window and it's a little slow to start to drag. The window becomes transparent as expected, but I don't know if I lose my mouse hold or what, but the dragged window remains transparent (like it's still held) and I can't click on anything else. The GUI is NOT frozen or hung, but the mouse clicking actions are ignored. I'm not sure if all keys are locked as well. I could use CTRL-Shift-ESC, but don't remember if I could arrow-key/tab through things. Maybe poll to see if the mouse is still being pressed on a drag.
There's not much we can do. What you describe sounds more like a problem in the x server.