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Take one of the .VOB files that's supposed to be progressive and open it in DGIndex. Press F6. What does the 'Frame Type' field say?
But in any case, it's in HCenc, because that's what's doing the encoding (and as I use HCenc separately of AVStoDVD, I know what its configuration files look like) - the new betas allow both *PROGRESSIVE and *TFF to be set, to help compatibility with some players (at least, that's how I understand it). The .ini you posted first contains both of them, but the video should still register as progressive, or mostly progressive, in DGIndex.
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