[Dovecot] Imap folders missing after updating

I just updated from 0.99.14 to 1.0beta2 on FC5 and my my IMAP folders have mainly disappeared in my Thunderbird client. All that's left is Inbox and Trash.

Is there some configuration setting that's now necessary to make the server think an account uses IMAP folders? The way it seemed to work before was that the presense of a Maildir directory in a user's home indicated IMAP. The new server seems to read the Maildir directory but it doesn't recognize all the folders.

Thanks.

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