HI,
The Unread Messages in Messages on the Mac compared to an iOS device is a bit of a known issue.
Apple use the word "sync" but it seems it is only "Display iMessage on all devices and computers" and not a full on syncing of actions taken elsewhere.
It seems that the Mac version is particularly bad at keeping up with what has been "read" elsewhere to the extent it is a separate issue.
I will wait to hear more.
8:47 PM Wednesday; November 21, 2012
Please, if posting Logs, do not post any Log info after the line "Binary Images for iChat"
iMac 2.5Ghz 5i 2011 (Mountain Lion 10.8.2)
G4/1GhzDual MDD (Leopard 10.5.8)
MacBookPro 2Gb (Snow Leopard 10.6.8)
Mac OS X (10.6.8),
Couple of iPhones and an iPad
"Limit the Logs to the Bits above Binary Images." No, Seriously