You and I are clearly using Emacs differently. I'd like to observe this behavior myself. Can you describe what you're doing? When you say partially obscured Emacs, what do you mean? Example, I almost always run Emacs with maximized frames (not full screen). I split a frame left and right into two windows L and R as Daniel had. I'll switch to Messages which partially obscures Emacs with. Then back. I almost always do this with the keyboard at least a hundred times per day. I've tried the pointer recently due to Daniel's prompting, but didn't see the issue.
-Stephane