Is your saddle too low or too far forward for your knee mechanics?

Do you need more float in your clipless set up?

It almost sounds like you were using loose shoes to substitute for more float, and when you tightened the shoes you "lost" your "float" and ticked off your knee.

I have a grumpy knee, but keep it happy with a saddle set farther back and super-floaty clipless and medial-wedged shoes.