I too have been unable to get a full POP download of everything in my Gmail account...a terrifying thought that this is all locked up with Google and there's no way for me to get my own mail out.
I can recommend. It took about half an hour to get my full GMail the first time, and later minutes to get the backup up-to-date.
Come to think of it, I haven't actually checked if it got my emails correctly :) I should probably reg a throwaway GMail and see if I can clone my current mailbox.
Back when I dumped my Gmail account I wrote a little Python program using imaplib to download and save everything into a database. The script got lost with my last system upgrade since it was in a temporary directory of which I usually make no backups. It's very easy to write though, just get yourself an imaplib tutorial and hack away.