Just noticed something else. The Include Dolby 5.1 checkbox on the HD for Apple Devices settings doesn't even seem to be working any more. I used to get files with AAC and AC3 tracks now they just seem to be AAC. This might be a result of the last update to Compressor.
I'm getting surround from the new Apple TV on movies from the iTunes store and Netflix as well as older home movies I've created. I just can't seem to make new files with a surround track.
This is all getting too complicated. Does anyone have an easy workflow to take a 1080p ProRes movie with 5.1 audio and generate the proper files (SD, 720, 1080) with proper tags and cover art ready to import in to iTunes and play on Apple devices.