Also check crank length.
Your new cranks might be slightly longer.

IF you are only having pain in ONE knee, obviously that knee isn't as good as the other one.

I have "bad" knees, with one having a more limited range of motion.
I simply have to use 165MM long cranks.
170MM and I'm on the edge of chronic knee pain. 175MM and my knee constantly hurts and cadence slowed down by 20 RPM.