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Sounds like a pretty nasty bug on the CS5 side. Since Media Encoder will use the Microsoft WMV APIs, be sure you have the latest stuff from Microsoft (though CS5 should have installed it). I'm assuming you're on Windows.
There have been reports of stability problems with Media Encoder for CS5, so you could try the Adobe forums to see if they have any workarounds.
To verify the problem isn't in your specific WMVs, collect a random few from the Web and try those.
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