In the most recent update, a glitch may occur with Thunderbird where you get two windows/instances when launching it from the quick launch bar.

The solution is simple - go to one of them, hit ALT-F4.

Don't use the "X" in the upper right, that'll close both of them.

Once you do this, two windows should not happen again. Read more:

http://forums.mozillazine.org/viewtopic ... &t=2623979