A user came into IRC with this problem today.  It seems to be caused by
the appindicator patch applied by Ubuntu, but I can't be totally sure.

If you quit Tomboy, and add it to your panel as an applet instead of
starting it in the way you normally start it, does the menu still have
the same problem?  I believe the problem will go away at this point.

If you then remove Tomboy from your panel, and start it the way you
normally start it, does the bug reappar?  If so, this is definitely a
bug with the appindicator patch and needs to be fixed by the Ubuntu
guys.

If you still have the problem even when running Tomboy as an applet,
we'll need to take a look at your .note files to figure out what's going
on.

-- 
Tomboy shows templates as notes
https://bugs.launchpad.net/bugs/664963
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