It doesn't matter if they are not split on correct chapters, you can still manually add correct chapters with multiple clips. Just make sure to delete the 00.00.00 chapter at the beginning of each clip that TMPGEnc will add, and then add the correct chapter marks within the clips. Also it doesn't join them into one mpg first, as it will author them directly into split DVD vob files. But maybe only 3.0 can do this, and not 1.6.
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