Installing Tiger was a disaster at first for me, mainly because of Apple Mail. I had previously installed httpmail to allow me to check Hotmail (though I rarely used it), and it seems as though that is where the problem comes from.
I did an archive and install, and after finishing, Mail refused to open (would open program, but nothing would happen). Later, I was able to access the new mail window. All the folders and mailboxes were there, but there was nothing in them! Thousands of e-mails, but nothing appeared.
So after some searching, I learned httpmail was the problem and propmtly deleted it from ~/library/mail/bundles/
Luckily, I had backed up all my mail, and I started to import my old mail. The old archive mailboxes imported fine, but I lost all my in POP account. For some reason, I had to import that mailbox as "other." So, eventually, I was able to recover it all. Lesson: Don't install the first day, and back everything up.