Have you tried turning the BEMF on the decoder OFF? That is the one huge thing that the decoder is doing that
the simple PWM board is not.
And yeah, I agree with Peteski, at this point, I'd be so curious that I'd open the engine, tack on some test wires, and
look at the decoder output on the scope while you actually run the engine. It would be great to see if the
wave form is noticeably different from a simple PWM square pulse, or if their frequency is super-high or low.
Oh! Were you scoping that PWM output WHILE you were running the engine? That could also be a huge factor. It could be
that the PWM doesn't look like that at all when you throw an inductive load across it.
Anyway... if one were curious... these are the things I'd be doing.