after my game times out or i log out of the game. there are sometimes up to three apps running and then i closed battle net. then log back into battle net only to find that it says the game is still playing. i go into task manager and find there the three apps are still running and i have to use task manager to close all the open apps and the game as well and then restart battle net to log into my account to resume playing the game.
Have you allowed Multiple instances in your Battle.Net App settings ?
Best of luck in your games !