One of our users is experiencing a notorious issue with Apple Mail, where folders do not appear where they should be.
This blog post sums it up the best - Hawk Wings » Blog Archive » A mendable Mail.app IMAP mailbox mess
From what I understand - to fix this issue, I need to give mail.app the correct IMAP Path Prefix. However, I'm having a bit of trouble figuring the correct prefix out.
*) Blank value - Folders appears outside the Zimbra mailbox (the globe thing as outlined above)
*) mail, ~/mail, Mail, INBOX - All subfolders disappear. Only the Inbox is visible.