I have used thunderbird 3.1.9 on win7. Actually, I have been used thunderbird since release 2, but I had never seen this problem.
When I use thunderbird, i usually meet disapearing of mail title, mail box(includ local mailbox) and menu. This problem may not happen with starting thunerbird but always happen after 1~2 hrs.
You will be more likely to get a response by posting this problem on the Mozilla Messaging Forum: http://getsatisfaction.com/mozilla_messaging
That is the place for Thunderbird support issues.
jswisher 18 Mar 2011