Thanks for the suggestions, I'll have to give those a shot.
I'm not at my PC at the moment so I can't test this out, but I was just reading about ATI's Avivo Video Converter that's included in the Catalyst Control Center. It uses the GPU rather than the CPU to convert video, so it can do it ultra-fast. Not sure if it does what I want to do, but I'll give that a go later.
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