Good news. I have a fix.
I found that IE 10's tear-off tabs triggered the bug so I could ignore it no longer. I did some investigation, found the combination of window flags which triggers the bug, and wrote code to find and modify those windows. Now I can have ipoint.exe, sidebar.exe,
and IE 10 tear-off tabs on Windows 7 and Alt+tab continues to work.
A full explanation and a download of the fix-it programs can be found here:
http://randomascii.wordpress.com/2013/05/28/alttab-bug-worsened-by-ie-10-but-fix-found/
Please let me know if this works for you. Comment here and/or on the blog post.
Wow, thankyou so much for finally fixing this, Microsoft!
Oh wait, it wasn't Microsoft that fixed it - it was a helpful 3rd party developer. Microsoft still haven't bothered to release a fix.
In any case, thank you for investing the time and effort into this, Bruce. After reading your blog post I'm curious - did you ever do any other experiments with these "ghost" windows, such as increasing their dimensions and bringing them into the visible area
of the screen to see what's actually on them? Seems like some kind of odd hack that the apps themselves are performing to hold focus (maybe for mouse-wheel interaction?). Seems kind of funny that the only apps we know of so far performing these hacks are
all written by Microsoft themselves...