I have noticed that programs with dark background don't copy well onto DVD. For example I saved James Cameron's Expedition Bismarck from home VHS to DVD. The dark backround underwater footage appears to flash bright and dark making it difficult to watch. Is this a motion estimation problem?
In the interests of eliminating all possible causes first, are you absolutely sure that you 100% disabled Macrovision during your transfer/digitisation? Arky ;o)
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But it is also true that dark scenes and water are difficult to encode without artifacts. Especially coming from a VHS source, where there will be an appreciable amount of noise in the video. Try some filtering (smoothing or denoise) before encoding to mpeg. You should find more in either the capture forum or encoding forum.