[D-tyme]

Have a work-a-round working...
ATV: 3.0.1
XBMC SVN: 27500
Media: Attached .mkv
Settings - Speakers = 5.1, Audio = Digital, AC3 = Yes, Downmix = No
Receiver: "Normal Surround" (aka Manual I suppose) - Optical input
With my receiver set to "Auto Format Detect" I get the typical 2 front channels only. When I made the change to "Normal Surround" all channels play, including the LFE. So I believe this is just a matter of the way XBMC is processing and/or delivering the signal; which my receiver can't classify. Hope this helps!

[mustardParty]

To you guys having issues with your equipment playing AC3 passthrough on your ATV's - in XBMC what does XBMC report in the movie info as the audio codec? I was having issues too and couldn't track it down initially, but I noticed that in XBMC all my 'apple TV' preset m4v files I created with handbrake report the AC3 track erroneously as AC3 2.0 when in fact it is 5.1 - but if I set my receiver to normal surround it will see and play 5.1 channels, and when the stereo track is played it switches to ProLogic II mode.

This only happens with m4v's though, I tested by making an m4v from a dvd with a good 5.1 track, and then re-encoded as an mkv with the same settings and XBMC saw and identified the audio codec correctly as AC3 5.1.