As an IMAP email service provider, it's always nice when email software that supports IMAP gets better over time.
Unfortunately Apple Mail seems to be doing the opposite. Basically we're noticing more and more problems with Apple Mail and IMAP support, and particularly with the way Apple Mail deals with the "sub-folders of Inbox" issue. This is slightly strange, given that the IMAP server we use is cyrus, which is the one that actually comes with OS X!
We're now recommending that Apple Mail users use the alternate namespace IMAP port to reduce the chance of future problems. Please see this blog post for how to change Mail App to use the alternate namespace port.
Update: A user has pointed us to a another blog post that might explain what causes the problem behaviour, and why it only occurs sometimes and for some users. As an alternative to switching to the alternate IMAP port, you might want to try the steps on this page first: