Using the thunderbird tray icon, only half of it is shown... Also had the same problem with some other progs (which don't come to mind right now) Reproducible: Always Steps to Reproduce:
How do you get the systray in thunderbird?
http://moztraybiff.mozdev.org/ like this
Ok, from what I see here, http://www.mozdev.org/source/browse/moztraybiff/source/components/?only_with_tag=v1-2 it uses a copy of eggstatusicon.c and EggSTatusIcon had a bug that was causing the icon to be 1 pixel wide. http://bugzilla.gnome.org/show_bug.cgi?id=172479 Maybe it's related, maybe it's not. Note that several apps have used a fork of eggstatusicon.c and are suffering from that bug.
This is supposed to be fixed in current trunk.