Thanks for clarifying. I had trouble with my right knee that my fitter thought was caused by my triple. The "tread" or width of triples can be too wide for some, which ends up causing IT band irritation. The right knee is often more irritated because the right pedal sits slightly farther from the bottom bracket than the left (because of the chainrings).
Anyway, I mentioned it on the off chance that you might be experiencing the same thing. Like you, my knee pain didn't start right away. I ended up getting a compact crank, and the problem was solved.
That said, yours could be due to any number of things, including your cleat. It could just be that you need a pedal system with more "float," or perhaps your SPD just needs to be repositioned. Hopefully, your fitter can figure it out.
Live with intention. Walk to the edge. Listen hard. Practice wellness. Play with abandon. Laugh. Choose with no regret. Continue to learn. Appreciate your friends. Do what you love. Live as if this is all there is.
--Mary Anne Radmacher