I have a strange issue since I updated my Thunderbird to 3.1.1. When I start Thunderbird it is launched two times means two Thunderbird windows appear.
I have no clue how I can solve the problem. I've tried to downgrade to 3.1 but the problem is still there. Seems my profile folder is messed up. If I copy the profile folder to a "new" Thunderbird portable I get the same problem.
I don't think this issue is specific to portable Thunderbird. There are random, rare reports of this for the mozilla-issued versions Thunderbird - there is no solution at present if I remember correctly.