Since one of the latest battlenet launcher patches, notifications no longer clear from the pop-out chat windows and the most recent response you have is a ‘New messages’ until you reply.
I recall this being an issue with one of the last battlenet launcher updates and a CS-Tech confirmed it as broken and it fixed following the next update. Could this be that the same problem has occured again?
I’m over in the EU but was told by a Game Master to report this issue here instead.