It probably is the same issue discussed in this thread...
https://forums.macrumors.com/threads/1455090/
If so, there is a workaround. You need to play the file, then hit select on the remote, change the audio track to stereo, then hit select again and change it back to surround. You should hear the surround sound then.
XMedia Recode doesn't encode the audio tracks right. It apparently marks them both as default which the aTV os no longer tolerates. You would need subler or a similar program to uncheck the surround track as being a default track for the aTV to handle it like normal.
I'm still trying to find a program like subler for windows, so unless you have a Mac, you may just have to deal with the workaround like I do.
Alternately, you could use Handbrake to re-encode the entire file. Others have noted that it encodes multiple audio tracks correctly, but the tradeoff is that handbrake re-encodes the video stream even if it doesn't need it. Theoretically, if you set Handbrake's quality high enough, then the video recode won't be noticeable, but it still wastes a LOT of time waiting for it to re-encode the whole file.
Jeff