Inbox empty in Mail 3 after 10.5.2 update and IMAP prefix "fix"

Question

After updating to 10.5.2, Mail detected an "error" in my IMAP configuration and asked me if I wanted to "fix" it by changing the prefix (or root or some such) to "INBOX". Since I assumed it knew what it was talking about, I said yes. It completely changed the structure of the folder list, and apparently this caused Mail to have re-download ALL the messages. It did this for about a day, with only new messages in my root Inbox appearing in the count for "new" messages. However, I could not access any of the messages of the Inbox, and STILL cannot three days later, even though all messages have apparently been downloaded. The messages are still there in the Inbox because I can see them from my Treo 755p IMAP mail client, as well as from the webmail interface for my email (www.fastmail.fm), but I cannot see them from Mail anymore; Inbox just appears as a blank mailbox. All the other folders are synced and have mail in them; there is no more downloading, and forcing a sync of the account does not download the 150+ messages I still have in my Inbox.
I do know that Mail has access to the Inbox, because while trying to force it download the messages I accidentally clicked on "Note" in the toolbar, and when I logged into my mail account from the webmail interface I saw a deleted message with the subject "New Note". (Fastmail shows deleted messages that have not been purged, by default). So, clearly Mail has write-access to the Inbox, but it's refusing to show me any of the existing messages in there, including several unread messages.

Answer 1

I have the feeling, that I found it. Here is what I did.
1. close Mail.App
2. turn off syncing in .Mac of mail accounts (not sure what its role is in this problem)
3. in the fastmail web interface, delete all "ghost" folders under that strange INBOX folder (moved messages first in correct folders); this folder suddenly appeared (I use web mail regularly, and I never noticed it before). I think apple mail created these somehow. "INBOX" disappeared when I finished deleting its childs.
4. Delete all files in ~/Library/Mail (except for the MessageRules.plist file, if you have one. Saves recreating your mail rules :o)
5. Then delete(!) the com.apple.mail.plist file in ~/Library/Preferences (it seems to use .mac to "remember" some of my email settings... my .mac account still existed when starting the mail.app, and while adding fastmail, it knew some of the info right away)
6. start up Mail and add fastmail
7. when/after syncing... click on each of the important mailboxes, and thru menu Mailbox | Use This Mailbox For denote what the box stands for (Sent, Trash, Junk, etc.)
Now, it seems to work. I haven't seen the "Change mailbox prefix" dialog, and my Inbox, Sent, Drafts, and Trash are neatly grouped by AppleMail.
Wow! It only took a couple of weeks !@#!#$@#!%@%^$^
Some observations:
1.Apparently there is something not standard about fastmail, and the IMAP settings, because the troubles I found on the net only seem to be fastmail related. Still, I find it strange that it causes problems.
2. I don't know, if I should turn on .mac syncing of my mail accounts again... I'm not sure what will happen.
3. Looking in Mail preferences... the prefix is INBOX (all caps); well, it works, so I'm not going to touch it. :P
Hope it helps!!
Melle