Emails not showing in Apple Mail inbox.

Hi All,
I can see emails being pulled into my inbox in Apple Mail but the inbox appears to be empty. The only way I can view them is to create a smart folder.
I've checked the Junk and Trash but they're not there.
Rebuilding the Inbox and deleting the preference file make no difference.
I've also removed and readded the account.
I'm using IMAP in Lion (I also have a Mountain Lion iMac but that's okay).
Thanks in advance for any help.

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.

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