Ok, on re-reading your question I think I may understand you now. But I'm not sure. So I'll just rattle off some general advice:

1) There's a feeling of "smoothness" that comes with a lot of practice at higher cadences. It takes time to develop the muscle memory; meanwhile you'll feel "jerky" and sensations like "coming off the pedal" or "not keeping up with the gear" are common. Advice: don't pedal so fast that you're bouncing or feeling jerky; just back off a bit and maintain a cadence that's quicker than normal but you can still apply power smoothly. It takes concentration and effort, for me the effort is mainly in my core to maintain stability, and my internal dialog is something like "smooth, quick, round circles"

2) Your knees could well be hurting from some other reason... ordinarily, higher cadences are better for sensitive knees. Rule out position / cleat / injury / overuse problems before you blame cadence.

3) At some point as you increase cadence, your pedaling efficiency will decrease / get choppy. That's not necessarily a bad thing or a good thing, it just is. Part of the reason to practice high cadence is to get used to higher cadences, but also to learn that you can pedal fast a choppy while still laying down effective amounts of power. The closing moments of a sprint, you are likely to be above your max effective cadence but you probably arent able to upshift... so it's good that you have practice and experience to let you know you can keep riding hard even if it's choppy and sloppy.

Hope this helps.