Adobe Media Encoder CS4 - Missing audio at the end of clips?

I'm running AME CS4 in conjunction with a Matrox H.264 accelerator card for MP4 encoding. Source material is .m2t and output is 720p as per YouTube spec.
I've been noticing recently that every other encoding job will chop a second or two of the audio from the end of the clip. ie. The audio will be fine until the last second or two of the clip, which is completely missing.
I'm lost when trying to figure out where to start troubleshooting. On a side note, I have noticed the same behaviour when transcoding .m2t files within Encore, which was part of the production bundle.
Any ideas? Thanks in advance!

I cannot guarantee that it is not a software issue. Sometimes Matrox is an easy "target." However, with several other Matrox users having similar issues, it does seem that Matrox might be the common element.
One of the issues with troubleshooting Matrox issues with PrPro is that few of the normal responders here have Matrox. Many tried the cards, and most unplugged them for various reasons. Some, like me, have never used them. That kind of limits the responses here, unless a Matrox-user, who has addressed such issues successfully, drops by with some tips.
Good luck, and please update the thread, especially if you do get a "fix." Others will benefit, and I will learn something new!
Hunt

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    Tagged date                      : UTC 2011-06-28 19:41:34
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    Format                           : AVC
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    Bit rate                         : 12.1 Mbps
    Maximum bit rate                 : 12.1 Mbps
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    Language                         : English
    Encoded date                     : UTC 2011-06-27 20:18:27
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    Bit rate                         : 128 Kbps
    Channel(s)                       : 2 channels
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