Had the same problem. Drove me nuts. At least for me this worked - in the Mail app I had 'to me' and 'cc me' filters checked. The 'phantom' (but legit) emails turned out to be all from a couple of group email lists that I was part of. After disabling those filters all is well. Also if you're sure there are no real emails awaiting your perusal after selecting the proper mail folder just use 'mark all messages as read' under the mailbox pulldown menu to eliminate the phanton count.
Hope this helps!