Due to lack of activity I did some more searching around, I didn't find
anything new and exciting. I did find a description of a slightly
similar problem, but the solution didn't apply to me (I'm not using the
relevant zoom plugins. See
http://ubuntuforums.org/showpost.php?p=3664399&postcount=13 for more.)

I should add that I have general mouse pointer problems which may be
related. I tried setting HWCursor off in the display device section of
the xorg.conf but that produced even less desirable effects - the mouse
pointer is not correctly composited when drug over composited windows.
Since I'm using xserver-xgl, that's pretty much everything but the
desktop. Moving the non-hardware cursor over avant-window-navigator, for
example, resulted in all kinds of trashing all over my dock. As a big
collection of composited windows this is not much of a surprise.

However, my mouse pointer also disappears when I hover over practically
anything, especially resize handles. When mousing over the window
gadgets it looks like there's something on top of it that causes it to
not be drawn, perhaps something tooltip-related? It seems like something
similar happens to the resize pointers. Sometimes they are visible,
sometimes not (usually not.)

-- 
Image corruption around the mouse pointer
https://bugs.launchpad.net/bugs/228861
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