This page indicates that this is the only way to get surround working for AppleTV:
For compatibility, the following is required:
Both tracks must be provided.
The AAC track should be first and it must be enabled.
The AC-3 track should appear after the AAC track and it should be disabled by default.
The AC-3 track must also use the appropriate MPEG-4/ISO standard.
Both tracks must be provided.
The AAC track should be first and it must be enabled.
The AC-3 track should appear after the AAC track and it should be disabled by default.
The AC-3 track must also use the appropriate MPEG-4/ISO standard.
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