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This is not surprising if you're using any converter based on FFmpeg, as it doesn't support all VC1 profiles or features (as I recall it won't do interlaced VC1). VC1 is a much more sophisticated codec than WMV3. You should probably transcode the VC1 to WMV3 first, but if you're going to do that, you might think about using a more robust converter. You don't mention what you're converting to, but if it's H.264 or FLV I'd try Sorenson Squeeze.
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