Welcome to my confusing and problematic world. We currently have 20-odd users on the Google Apps domain. 3 of them are using Apple Mail to access their mail. 1 is having problems. The only thing different about this user is that we imported messages in from Outlook using the Google mail importer. This is the only thing I can think. The importer seemed to ignore certain folders, even if we retried, and it created folders as inbox/insurance_ etc. I changed all the folders to INBOX in caps, as that is what Mail preferred, and removed the trailing underscore.
This is the only thing different about this user.
On a web browser looking at Gmail, I have:
Inbox
Starred
Sent Mail
Drafts
--------
[Imap]Drafts
Apple Mail To Do
Deleted Items
Deleted Messages
Follow Up
INBOX/folder1
INBOX/folder2
INBOX/folder2/folder1
etc...
INBOX/Folder113
Junk E-mail
Misc
Priority
Sent Messages
4 More (containing Chats, All Mail, Spam, Bin)
I did another "Account Info" and got this:
http://gallery.me.com/rtaxerxes/100023/Screen%20shot%202009-11-04%20at%2010.19.5 9%20PM
You'll notice, now it does have an Inbox. But the folders it says are 0 messages and 0 KB do actually have stuff in them on the web browser.