Guys, same here...
My company's IT department runs Exchange: 14.3.123.3 (from web app info) and my Mail is 7.3 on 10.9.4 Maverics. So far my default Inbox gets mails properly in time, it just occasionally fails to mark some messages as read once clicked on them. That would be ok, I could make it done via right-click menu. But there is a serious issue with sub-folders in the default Inbox. Some of them contain NO messages while I can see tens of them via WebApp on Exchange server in the same sub-folder. Some of subfolders show several messages selected by random (I can't see any pattern here) and even Mail Search window cannot find messages that apparently are existing on the Exchange server. Finally, when I dragged email from my default inbox folder and dropped it into the sub-directory, it disappeared. Yes, it did.... Fortunately, the Exchange server has apparently got the notion because the moved mail can be seen now in proper sub-directory via WebApp.
I tried literarily all suggestions and tricks I found here, re-enabling email account, rebuild function, reseting PRAM or SMC or whatever else. The problem persists and virtually, I cannot use subfolders in Mail at all. By the way, our IT guys had migrated my mail box to newer Exchange and the problem started just then.
Good luck to everyone here so Apple hopefully listen to our complains. (via user feedback form at least)