I don't have an answer, but a suggestion would be to start in safe mode and then run through the diagnostic steps given in the second of these two links
I'd be inclined to suspect an incompatible plugin is the cause - maybe a third party A/V or Spam-detection program? What security software do you have on the machine?
Safe Mode - MozillaZine Knowledge Base
Standard diagnostic - Thunderbird - MozillaZine Knowledge Base
PS - what is actually doing the Spam filtering? Is it just the default Thunderbird filter, or have you installed a plugin like Spamatu or Habu?