Pilates has helped me in every other part of my body pain besides my knee pain

I’ve talked to multiple instructors about it and they all say to make sure I’m using the knee pads when on the mat,make sure that I’m flexing my toes, and using my glutes.

I do all that, and I feel like they seem to think despite me telling them that the knee pain is coming from the mat work and when my knees are literally touching the mat- however, my hypothesis is that it’s all this pulsing on the reformer. I try not to ‘bounce’, but it his repetitive teeny pulsing motions feels not good for my knees/like it’s hurting my knees?

Is there something else I’m not thinking of that my instructors didn’t mention to help here with my knees? Or is the pulsing kind of doomed to hurt them?

I’m happy to deal with the knee pain since everything else is doing better than it’s been in forever, but figured I’d ask!