Adobe Media Encoder CS4 doesn't encode audio

I'm having trouble getting the Adobe Media Encoder CS4 to
work properly. I have tried multiple files of different lengths but
end up with the same output. Nice video encoding, but the audio
starts and then cuts out after a couple of seconds. The longer the
video, the shorter the audio works. The logs don't report any
issues. Anybody have any ideas?

I have the same problem just trying to crop an FLV. (Encoding from FLV to FLV on Snow Leopard).
The audio just dies about 5 seconds in (the clip is 28 seconds long).
Sucks. I wish I could find the original .mov
I wish I wasn't forced to recompress the audio.
I've tried various settings all night - most settings result in no audio whatsoever.
Also, Media Encoder alters the mod date of my original file. Why?
I'm really frustrated with this software.

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    Oh hai!
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    Please help, I can't do any video editing, because of this problem. And sorry for my english, ask if you didn't understand something. =)

    Hello, this is terrible problem, which i found in CS 6 softwares ...
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    2.by necessity to begin work in another windows profile you again WASTE YOUR TIME because of learning and migrating all other profile modifications, which i see really unaccpetable. Adobe means, this solution of repair is ok, and they did not do till today any steps of creating some "clever" solution.
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       I am not IT, but ..does it seems so hard to create this ? Adobe IT developers should know their systems, and should create such utility tool really easy.
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    •C:\Program Files(x86)\Adobe
    •C:\Program Files\Common Files\Adobe
    •C:\Program Files(x86)\Common Files\Adobe
    •C:\ProgramData\Adobe
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    •HKEY_CURRENT_USER\Software\Adobe
    •HKEY_LOCAL_MACH INE\SOFTWARE\Wow6432Node\Adobe
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    ==exporting of any sequence/raw/AE link video material from premiere via "queue" (Encoder) (profile B) : export WORKS
    ==exporting of any sequence/raw/AE link video material from premiere via "queue" (Encoder) (profile A) : export DOES NOT WORK ! ! !
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    this issue should be some "broken" connections between encoder and premiere, which refuses to "take material" from it and encode.
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    what i do NOT expect from Adobe:
    to get from Adobe advice of kind : you have to reinstall full software in new admin profile. sorry , we do not know the solution, because we do not know, how do behave our software.

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