Mountain Lion Breaks Apple TV with 5.1 Surround Presets in Compressor

First let me preface that I am working with two different systems and have recreated the issue on both of them- 2009 13" MBP and a 2011 Mac Mini Server.  The issue is caused by Mountain Lion (I know, shouldn't update production systems and all but it happened so I thought I'd give folks a heads up).
In Lion, if I used any of the Apple TV presets in Compressor and ticked the "Include 5.1 Dolby" check box, viola I had my 5.1 surround.  However, when I attempt this in Mountain Lion, the 5.1 audio is created but never muxed into the final m4v that is created.  I have even gone back to old projects that worked fine with this preset and still cannot create a m4v with 5.1 audio. To test this, my wife's MBP was still on Lion as of yesterday so I grabbed a test file and exported to Apple TV 3rd gen with 5.1 and it worked.  I upgraded the system to ML and used the exact same file and this time it only created an m4v with stereo AAC and no secondary track.
Also, exporting directly from FCPX does not work either.
As a workaround, creating a standalone 5.1 mix is possible (as I learned when I needed to create a DVD as well for this project) but then I would have to use another program to mux that together with the m4v, which is not as convenient as just using the preset.
I have submitted this as a bug to Apple but I encourage anyone experiencing this issue to do the same.

Overrider......Just drag and drop your movies on iTunes from the folder you designate as the output for handbrake. iTunes does a little processing of the movie during the copying (check the size using
Get Ifo" on the files to see the decreased file size in iTunes.
If you don't want to buy FCP or FCPX try just ripping with MakeMKV (free) I use it for DVD and Blu-Ray... very intuitive, very powerful.  If the movie has a DTS soundtrack, for $10.00 AUNSoft's MKV Convertor does a stellar job.  final processing either way is free with Handbrake,, using the applicable preset as you all note.  The only trick is Do Not designate the AC3 track with a checkmark in Subler, Meta-x or whatever you use.  It will be a passthrough that you will see.
No complicated software needed.. very simple.  I have over 4TB of HD movies with 5.1 sound streaming to my ATV done this way.  Don't overthink it... see my earlier post for movies already done... Subler can open and let you fix these also if you need to.

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