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The reason I ask is that when I delete images using VD the resultant image doesn't seem to take as much waveletting as the original before oversharpening speckling occurs
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I don't think that's possible - there must be something different that you're doing - i've noticed some funny quirks in registax 3 sometimes that could easily provide strange images if I hadn't noticed it.
Virtual dub just loads and saves the raw frames, it shouldn't change what post-processing you can do. I haven't noticed that problem myself.