That's my question...so my receiver is decoding MP3 and AAC files? I don't think so. So the ATV is decoding the MP3 and AAC files to PCM?
You are connected to your receiver by the RCA connectors or the optical connector? My understanding is the RCA is a decoded (analog) signal only, while the optical port can do pass-through (digital). (Someone please correct me if this is wrong.)
I'm sure there are receivers that can decode digital MP3 (since car stereos can do it), but I am unaware of any that can decode AAC 5.1. AC3 yes, but not AAC 6-channel.
You might try downloading files from this page to see if you're getting 5.1:
http://www.diatonis.com/downloads_dts_ac3.html
I can't try it because my ATV receiver is an older DPLII model that can't do DD or DTS. (My home theater is run by a Mini with an Onkyo 5.1 receiver.)
Presumably, the optical port on the ATV will do passthrough - the passage of the audio data in its native code. Apple's DVD Player app does this (but it's not on the ATV) and is used for DTS and DD 5.1 on computer (i.e., Mac) based audio systems connected to receivers that can decode these formats. Perhaps SunRiser can add to this?