I'd like to provide some findings regarding the strange focus
handling:
emacs -q --no-site-init
C-x 2
C-x b bla (make it easy to recognise the two frames)
put the mouse on the toolbar to create a popup works fine.
Alt-Tab (using XP to switch frames)
put the mouse on the toolbar to create a popup will NOT work right.
(i do not even see the popup but the first frame with
the *scratch* buffer pops up while the second with the
bla buffer still has input focus.
Maybe it is the second frame with the bla buffer that
pops-under??? if this is possible..)
Now try doing the same thing but using C-x 5 o to switch the frames will
cause the popup to work just fine. Does C-x 5 o some thing special
compared to Alt-tab?