Why is migration from Mac Thunderbird to Mac Mail not working properly?
A friend of mine had a similar problem when migrating local mails from a POP mail account from Windows XP (Thunderbird) to a Mac (Mail.app).

This is what we did:


Create an IMAP account (we chose aol.com, gmail.com is another good choice).
Configure the new IMAP mail account in Thunderbird.
Drag and drop all mails from the local account to the IMAP account. This may take a while.
Configure both your current mail account and the IMAP account in Mail.app.
Copy the files back to your current mail account (again, drag and drop).


(You may consider keeping the IMAP mail address...)

This may be easier than troubleshooting why the import doesn't work properly.