Bike fit / correct riding position

My left knee has started tracking all over the shop when riding clipped on my road bike. Always used to be spot on. I have been riding my commuter a lot recently which has flat pedals and a slightly different set up overall. Will this correct itself, I only noticed it on one 2 hour ride after a week without using that bike? Cleats are not worn and have not moved on the base of the shoe. My knee hurts now.

This has only gotten worse. My left knee tracks all over the shop, it seems like I really raise my heel at the bottom of the pedal stroke and it seems there is a total dead spot at the bottom too. Moreover it hurts to ride on. Any advice? Was fine with the same fit a month ago. Single pedal drills? New fit?