[Dovecot] Missing Mailboxes

I upgraded from Fedora 4 to 5, which took me from dovecot .99 to 1.x. When I started up Thunderbird, I could not see any mailboxes other than Inbox. I am using Maildir with postfix. I re-installed .99, and all the mailboxes are back. I looked at the wiki on Missing Mailboxes, but I am not sure what I have to fix, and I do not really want to re-install the 1.x version and mess around, as I will mess up a number of other people. Clearly, I am not an expert, so if anyone can can help, I will be most appreciative!

Jim