Post your script. It's not clear what exactly you are doing there. In particular, since it seems you're actually doing IVTC ....
Fades generally are problematic. As far as MVTools are concerned, try different DCT modes - they can help to get better matches. (For some fun, try blocksize 16 together with DCT 1. No, nothing is broken ... it *IS* *THAT* slow. Really.)
But even then, it's still a fade ...
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