I have the same problem, as does a coworker. It happens, for instance, if I click on another mailbox (such as Junk) then go back to the inbox. Our company uses Exchange. Quitting mail usually fixes it. A rebuild of the mailbox will too. Only happens on my Mac at work, not my Mac at home (connected via VPN).
Another problem I have is with mail not syncing. Mail I have deleted from another device (such as on my Mac at home or my iPad) does not get deleted from my inbox at work. Sometimes they'll go away when I click on them. Other times they won't go away and the only way to delete them is to rebuild the mailbox.
And lately I have had problems with attachments. Attachments sent from my Exchange account at work show up as .eml attachments in my iCloud account and mime attachments on my iPad or as a string of characters (20-30), not as an attachment. This happens whether sent from home or work.
I have our IT department looking into the third problem (which is the most vital one for me). I'll report the other two annoying problems and see what they can figure out.
I too am having a very similar issue.
I have a 13'' MacBook - updated to 10.8.2 using Mail 6.2.
I set up Mail to new IMAP account and archived old emails. It was working great...syncing to all my devices. Now Mail indicates that there is mail, but when I select Inbox there is nothing there. I can get mail from other devices, so I can definitely pin-point the issue being Mail.
Even mail that I have archived 'On my mac' is not available.
very annoying situation....any fixes??
Again, same problem here. Mail 6.5 on OS X 10.8.4. Connection doctor shows good connection to Exchange, no change in settings, clicking off Inbox to another mailbox and then returning to Inbox causes messages to disappear ("0 messages, 56 unread"). Restarting does not always clear it. I am getting some EWS error messages in Console, another posting recommended deleting account and EWS cache folder, but that doesn't seem to help. Gmail works fine within Mail, Exchange works fine on iPhone and within Outlook. This problem is older than OP, I've seen it go from time to time. Exchange 2007.
Hopefully someone can illuminate/address this, the lack of response to earlier postings is .... disturbing.