Music Does Not Play using Remote APP

Still having major issues with the Remote APP for the iphone. When I play a movie using sapphire and try to play music afterwards it will not play. I have had to reboot my ATV in order to make it work properly. Please help.

Also I notice it does not currently control Sapphire and the only thing that will is the standard remote. Anything in the future to support this?

This has to do with the AC3 passthrough output of the HDMI. When I output the analog from the ATV I get music. When a movie is played it seems to shut off the digital signal for music. How can I fix this?