I was trying to import messages to Mail from the Unix program elm, and I ran into a few problems. At first, when I tried to import the elm mailbox only the first message would be imported. I fixed this by opening the mailbox file in BBEdit Lite and saving it as a different filename. I'm not exactly sure what this did, but it allowed me to import about half of the message.
To fix the rest, I went into ~/Library -> Mail -> Mailboxes, and control clicked the imported mailbox and selected "Show Package Contents." From there, I opened the "mbox" file in BBEdit and removed all of the '>' characters from the beginnings of "From:" lines. After this, all of the messages imported without a hitch.
So if you're having trouble importing mailboxes, you might want to try this.
[Editor's note: I have no idea if anyone will find this useful or not, but I figure if you're stuck trying to import a mailbox, having this knowledge around can't hurt...]
Mac OS X Hints
http://hints.macworld.com/article.php?story=20021213112329479