I think I've figured out why the package manager seems to trip it up.
It presents a unique case, where both the contents of /usr/share/pixmaps
and /usr/share/applications change at the same time, or at least in
between menu browsing.

Here's an example that I've found to rigorously reproduce this bug:
0. (Gnome ,menu must be on bottom panel.)
1. Browse menu until bug no longer is present.
2. sudo cp /usr/share/applications/totem.desktop 
/usr/share/applications/test.desktop
3. sudo touch /usr/share/pixmaps/test.png
4. Browse menu and notice that the bug appears

The important thing is that you don't browse the menu in between steps 1
and 4, because just doing either step 2 or step 3 does not seem to
produce the bug.  Just when both happen in between menu browsing does it
occur.  Also, steps 2 and 3 can be performed in reverse order, i.e. step
3 then step 2.  And also, it seems that to reproduce this, it needs a
real ".desktop file" in the applications directory, whereas a phony
touch'ed png file will suffice (although so will a real image) in
triggering the bug.

And, of course, to reproduce it again:
1. Browse menu until bug is no longer present
2. sudo rm /usr/share/applications/test.desktop
3. sudo rm /usr/share/pixmaps/test.png
4. Browse menu and notice that the bug appears

-- 
gnome-panel doesn't show all menu items
https://launchpad.net/bugs/30146

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