I ran into a problem, when I built my new mail server environment. I used the backup files to create the maildirs of the accounts, and I experienced my mailbox was empty in my imap client, however there were a lot of mails in it.

maildrop -V 3 -d nick@example.foo

throwed the next message:

Unable to open mailbox

despite of permissions was good.

People are disposed to exclude tmp directories from the backup files, but tmp is very important in maildir. Without tmp directory the mailbox looks empty. So modify your backup script to store the tmp directories without content to avoid the latter headaches.