Very surprising to me that Microsoft has NOT yet even acknowledged this as a bug.
Agreed. The "update" that causes this bug is IE9. Remove it as you would any other update, and the problem should go away. Worked on home and work computers as well as laptop.
IE9 may help trigger the bug in the OS shell (explorer), but I don't think it is the cause. I remember seeing this bug back in the Windows 7 beta in 2008, which is before work on IE9 had even started.
For me shutting down ipoint.exe and and sidebar.exe is enough to resolve the bug. I wouldn't be surprised if other programs can also trigger it, but IE9 is not enough by itself. I've had IE9 installed since it released and the bug only happens if ipoint.exe
or sidebar.exe is running.
If you find another program that triggers the bug -- a program that if you kill it with task manager the bug goes away -- please report it, both here and at:
http://randomascii.wordpress.com/2011/10/16/alttab-depth-inversion-bug/