From what I have read, which may be outdated too...
The AppleTV 2 will output 5.1-AAC as stereo, not 5.1 LPCM. I think that there may be a muxer that converts that 5.1 AAC into 5.1 AC-3 (Dolby Digital).
The problem is that the your sources are encoded for PS3 and WDTV (maybe?) and HTPCs.
The PS3 can't deal with the AC-3 (DD) or the m4v container. The people making these files usually encode the 5.1 AAC at the same bit-rate (448 or 480, i forget) that the original 5.1 AC-3 (DD) was encoded, therefore they are not really shrinking the files by choosing AAC, just making them PS3 compatible.
MKVtools, written by one of our forum members.
MP4 with 5.1 AAC to MP4 (video pass-thru, untouched) with sound converted to 5.1 AC-3 (DD) with a 2 channel AAC to maintain ipad/iphone/ios compatibility.
I'm testing for you right now
UPDATE
I just did the conversion, took 17 minutes on my 2GHZ Core2Duo Mac Mini with 4GB of RAM
MKVtools
Gobbled up about 1.5 GB of RAM (speeds up muxing)
-Ran 2 mencoder processes, i think one for converting the 5.1 AAC to 5.1 AC-3, and the other for converting to 2 Channel AAC (for iOS compatibility)
These processes ran at 55-70% of 1 cpu each.
Then mp4box runs through 4 sequential steps, the first 2 using 20-30% of one cpu
The steps 3 and 4 using 8% or less of one cpu
When it was all done 17 minutes later, MKVtools promptly freed up 1.5GB of RAM that it needed
Now for the file details
Original
MP4
Video Stream
Codec (Human Name)................................AVC
Codec (FourCC)....................................avc1
Codec Profile.....................................High@L4.1
Frame Width.......................................1 280 pixels
Frame Height......................................688 pixels
Frame Rate........................................23.976 fps
Total Frames......................................132932
Display Aspect Ratio..............................1.860
Scan Type.........................................Progressive
Color Space.......................................YUV
Codec Settings (Summary)..........................CABAC / 4 Ref Frames
QF (like Gordian Knot)............................0.134
Codec Settings (CABAC)............................Yes
Codec Settings (Reference Frames).................4
Video Stream Length...............................1h 32mn 24s 381ms
Video Stream BitRate..............................2 825 Kbps
Video Stream BitRate Mode.........................VBR
Bit Depth.........................................8 bits
Video Stream Size.................................1.82 GiB (87%)
Audio Stream #1
Codec.............................................AAC
Codec (FourCC)....................................40
Audio Stream Length...............................1h 32mn 24s 533ms
Audio Stream BitRate..............................425 Kbps
Audio Stream BitRate Mode.........................VBR
Number of Audio Channels..........................6
Audio Channel's Positions.........................Front: L C R, Side: L R, LFE
Sampling Rate.....................................48.0 KHz
Audio Stream Size.................................281 MiB (13%)
Audio Stream Language.............................English
New File:
General / Container Stream #1
Total Video Streams for this File.................1
Total Audio Streams for this File.................2
Video Codecs Used.................................AVC
Audio Codecs Used.................................AC3 / AAC LC
File Format.......................................MPEG-4
Play Time.........................................1h 32mn
Total File Size...................................2.22 GiB
Total Stream BitRate..............................3 435 Kbps
Video Stream #1
Codec (Human Name)................................AVC
Codec (FourCC)....................................avc1
Codec Profile.....................................High@L4.1
Frame Width.......................................1 280 pixels
Frame Height......................................688 pixels
Frame Rate........................................23.976 fps
Total Frames......................................132932
Display Aspect Ratio..............................1.860
Scan Type.........................................Progressive
Color Space.......................................YUV
Codec Settings (Summary)..........................CABAC / 4 Ref Frames
QF (like Gordian Knot)............................0.134
Codec Settings (CABAC)............................Yes
Codec Settings (Reference Frames).................4
Video Stream Length...............................1h 32mn 24s 378ms
Video Stream BitRate..............................2 825 Kbps
Video Stream BitRate Mode.........................VBR
Bit Depth.........................................8 bits
Video Stream Size.................................1.82 GiB (82%)
Audio Stream #1
Codec.............................................AC-3
Codec (FourCC)....................................ac-3
Audio Stream Length...............................1h 32mn 24s 512ms
Audio Stream BitRate..............................448 Kbps
Audio Stream BitRate Mode.........................CBR
Number of Audio Channels..........................6
Audio Channel's Positions.........................Front: L C R, Side: L R, LFE
Sampling Rate.....................................48.0 KHz
Bit Depth.........................................16 bits
Audio Stream Size.................................296 MiB (13%)
Audio Stream Language.............................English
Date of Original Encoding.........................UTC 2011-04-08 23:47:39
Audio Stream #2
Codec.............................................AAC
Codec (FourCC)....................................40
Audio Stream Length...............................1h 32mn 24s 448ms
Audio Stream BitRate..............................157 Kbps
Audio Stream BitRate Mode.........................VBR
Number of Audio Channels..........................2
Audio Channel's Positions.........................Front: L R
Sampling Rate.....................................48.0 KHz
Audio Stream Size.................................104 MiB (5%)
Audio Stream Language.............................English
Sorry I can't verify this works (AC-3) on the AppleTV 2 at this moment, but it transferred to my iPad 1 and is playing flawlessly.