Here's one link about the subject: https://support.mozilla.org/en-US/questions/1132064
You'll find more with https://www.google.nl/search?q=thunderbird+master+password+twice . After studying all, see if you need to post a bug on bugzilla or their support forum.
Ive been using TB and FF both w/master PSWDs for several years under xp and now win7.
About two years ago, TB started asking for my mstr pswd twice. This was not a new install it just started happing with no known changes made to TB or o/s. As soon as I enter and click button, it pops up again and I need to enter my mstr pswd again. Then I get my emails and all is normal, until the next time TB is opened, then again i need to enter my mstr pswd twice. Ive wiped my HDD and reinstalled o/s and all applications twice since this started happening and it continues to ask twice. Ive even tried changing my mstr pswd.
It happens with FF open or clsed.
FF, TB, and win7 all up to date.