No audio in Apple TV on certain rips?

Suddenly I am noticing on certain rips that I have no audio when played through Apple TV. When I try in Quicktime, audio is great.
The file is a M4v recorded with AC-3 audio ripped with Handbreak.
Thanks to anyone for the help as I could really use it.

Thank you so much. This is so on target with what I have been going through.
You have saved me additional hours of work.