I'm sorry, I meant to refer to its implementation of Maildir. Is this the standard format? I had a lot of trouble getting this format to work well with Apple Mail. I'm pretty sure its Mail's issue as thunderbird works perfectly.
Eh... I don't think that this is an issue related to Mail.app. It depends on how it is served by the IMAP daemon. But I never experienced any problems when using together Courier-IMAPd, Maildir as the storage backend and Mail.app as the frontend.
Regards, Philipp Kern