Metacity gets confused by having xinerama and two monitors with different
resolutions.  Specifically, if I have a panel on the smaller monitor, and
move that panel to the bottom, metacity kinda goes bezerk.  It can only
place windows in the middle area of either screen wrt y axis.  With enough
fiddling one can get the panel back on the top or left, and then everything
is ok again.


Lesser points:

Also, a related concern is that a panel on one screen prevents windows from
being positioned in the location of that panel on the other screen.  So say
one screen has a panel on top, now I can't put windows all the way to the
top on the other screen.  The work-around is to (a) get over it (b) put
panels in the same place on both monitors.

Finally... well, I guess this is a gnome-panel thing, but with 2.2 you
could specify what screen you wanted the panel to appear on, but now that's
gone.  I discovered you can still control which screen it displays on by
dragging the panel.