Tarq57, This got me wondering how Thunderbird works, so I looked at some of the help pages. One thing which just might be of relevance is that compressing folders or even deleting them doesn't get rid of them, they just get bigger until the program starts struggling. Compacting them however does. According to Mozilla most Email programs do this automatically, wheras with Thunderbird you have to do it manually, or select it to automatic from the Options menu. I followed their instructions to open folders into Notepad and found large amounts of random letters/numbers in between some readable messages.
I know this won't help your situation, but it might shed some light on goings on behind the scenes.
Regards.