I use iMessage/SMS on my Mac linked from my iPhone, I have been having issues with it on my Mac lately with the unread count being incorrect.
It says that there is a message unread when its been read on both my phone itself and my Mac. I have even deleted the conversation from my Mac but the count is still there.
It seems to be from the SMS messages I receive, I have tried enabling and disabling iMessage on Mac but that did not fix it.
(I have the latest versions of Mac OSX and iOS installed)