Video/audio editing bug in Media Encoder

I have a large MOV file that contains multiple film
presentations, one after the other. They are separated by a few
seconds of dead air. I'm using Video Encoder's built-in edit tool
to slide to the end of a presentation and then export that to FLV.
Using my arrow keys, I can pinpoint the exact millisecond I want it
to stop.
However, when I export these to FLV files, audio (but not
video) continues to play for several seconds even past the point at
which I had set the cutoff.
I tried duplicating the same thing using Flash 8 Video
Encoder, and didn't have a problem. It only appears to be an issue
with Flash CS3 Video Encoder.
Can anyone duplicate what appears to be a bug?

Screenshot of Premiere Export (fills screen):
Screenshot of Media Encoder export: (notice the pillar-boxing)

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Screenshot of Premiere Export (fills screen):
Screenshot of Media Encoder export: (notice the pillar-boxing)

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I got Creative Suite 4 (Production Premium). I usally uses AE and PrePro, saves the project and uses Media Encoder to export the footage. My filmcrew got a Sony HDR-200 (I think) who saves in AVCHD, m2ts full HD.
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Computer (Costume Made):
Asus PQ53 Deluxe
Intel Core 2 Quadro 3.0Ghz
8GB DDR3 1066mhz RAM
eVGA Geforce GTX 285 (1GB GDDR3)
Corsair 650W
2 huge Fans...
NB: An hour before posting this, all BIOS were updated.

Please ask in the AE forum.

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* * * MediaInfo Mac 0.7.36.0 file analysis report.
* * * MediaInfo Mac is ©2010 by Diego Massanti - http://mediainfo.massanti.com
* * * MediaInfoLib by Jerome Martinez - http://mediainfo.sourceforge.net
Created on: 8 jan 2011 17:50:03 CET
Report for file: test_b3_0.mp4
General / Container Stream #1
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    Total Audio Streams for this File.................1
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    Audio Codecs Used.................................AAC LC
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    Total Stream BitRate..............................2 122 Kbps
Video Stream #1
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    Codec (FourCC)....................................avc1
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    Frame Height......................................480 pixels
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    Display Aspect Ratio..............................16:9
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    Scan Type.........................................Progressive
    Color Space.......................................YUV
    Codec Settings (Summary)..........................2 Ref Frames
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    Codec Settings (CABAC)............................No
    Codec Settings (Reference Frames).................2
    Video Stream Length...............................55s 760ms
    Video Stream BitRate..............................1 995 Kbps
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    Video Stream Size.................................13.3 MiB (94%)
    Video Stream Language.............................English
    Date of Original Encoding.........................UTC 2011-01-07 13:20:32
Audio Stream #1
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    Codec (FourCC)....................................40
    Audio Stream Length...............................55s 808ms
    Audio Stream BitRate..............................125 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.................................854 KiB (6%)
    Audio Stream Language.............................English
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http://forum.videohelp.com/threads/169292-How-to-stream-live-TV-using-Windows-Media-Encoder
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been digging deeper and deeper into video and audio production and editing.
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