Long time ago, but I think the best method may be to convert your video file to a TGA or BMP image sequence (1 per frame) and make sure your alphas are still applied. Then convert that image sequence to AVI and use Virtual Dub as usual to convert that to VP6. RadVideo Tools should be able to perform everything until you need VirtualDub.
It may be some limitation of the third party decoder/encoder that causes loss of alpha so I may be way out on this one.
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