Thanks for the reply. That is the only other variation that I can think of. I was using SPD's, now I have Look pedals. Which I love!
But maybe the float is different and my knee doesn't track the same.
I didn't notice anything immediate when I got the new bike. It was more gradual. After about the 5th ride of 25-30 miles I started noticing it.
Which now that I think about it, makes sense that it would be the pedals.