Encode Dobly Digital 5.1?

I used to have an AppleTV and converted a lot of material into the .m4v format that had h.264 video and AC3 5.1 Audio in them. I've since sold my AppleTV and want to convert these files into .m2ts files using Compressor for playback on my PS3. I can't extract the existing AC3 file into an elementary stream so I think I'm going to have to re-encode it.
When I add the files to Compressor it correctly recognizes the audio as AC3 5.1. I select the Dolby Digital Professional Setting and it creates a 5.1 Channel file - but I only get audio out of the Left and Center channels.
Any help?

The solution to my problem was with Perian. Perian, which was being used for playback when encoding, was defaulting into Dolby Pro Logic. When I changed Perian's settings to Multi-channel output I got six active channels.

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