I switched to Speedplay Frogs and the knee pain disappeared, but I've been advised by a bike fitter/physical therapist that the unlimited float in Frogs makes for an inefficient pedaling path. He refit me for SPDs, and...the knee pain came back, so much as I'd like to make them work for me, apparently I can't.
Call me crazy... but what DOESN'T CAUSE ME PAIN... is what works for ME.

Is this guy your regular doctor, or just someone who works at the bike shop and physical therapy?

Do what makes your body feel good. If you didn't have knee pain with the Speedplays, what was the problem? Oh, the inefficient pedaling path. ????

I had knee pain, I switched to Speedplays, when I ride my foot typically doesn't float around while I am pedaling... and I can do a good 25 miles with a 17.5 mph average. Sure, I'm not totally hauling butt... but my pedaling is efficient... in my book.

Best of luck with finding what works for you. But I say, go with what doesn't hurt.