I had similar problems with Mail on Mavericks - at least - I have one folder -Jobs- in 'On my mac' containg a lot of subfolders that receive emails for customers according to rules...
The containing Jobs folder didn't show mailcount after upgrading to Mavericks.
After searching the web I ended up here and was just clicking around in mail...
Suddenly I clicked right to the line 'ON MY MAC' in the Mailbox list and there was this 'HIDE" command (feek dumb but didn't even know it was there...)
After clicking it and afterwards clicking SHOW again, suddenly the correct message-count was also on my containing Jobs folder...
It can well be that I did something stupid at some point but perhaps someone else is actually having the same minor problem
cheers