I think this might be along the lines of the problem reported in ticket number 205, but different.
I closed a chat window with command + w as I had finished chatting. As I did this my friend replied so the mesg came through with the new mesg sound but didn't display the window. At this point the username was flashing in its unviewed content style. I double clicked the username to open the chat wndow to view what they had said and username just kept flashing. They signed off right after and it is still flashing. Tried sending a mesg to them to stop flashing but to no avail...