Here's how I got Mail to see all my old mail:
Leaving my ~/Library/Mail folder in place, I trashed -- actually, I moved it out to my Desktop to make sure this worked first -- my ~/Library/Preferences/com.apple.Mail.plist file then re-created my accounts through Mail. As the accounts were created, the mailboxes would show up with all the previous messages still intact.
May not actually be a solution, but it seems to have worked for me. Before I did that Mail would just crash when I tried to open it unless I nuked everything first.