Unread message in Messages not being set as "read"
This problem is fixed in a new release of 10.10.2


I'm currently running 10.10.3 and am having this issue again, so not fixed in 10.10.2 unfortunately. Have experienced in the past, major pain.

The following works for me every time


  In the Finder > Go Menu > Go to Folder type (Copy and Paste) ~/Library/Preferences into the Dialogue box.In the Preferences find the com.apple.imessages.bag.plist and drag it to the Trash.


(found on https://discussions.apple.com/thread/4486753?start=0&amp;tstart=0)

Then reboot the machine.  The post says to reboot messages but I always have to reboot the entire computer for this to work properly.