I put some FSA carbon cranks on my bike last week, and got my first real miles over the weekend - about 150 total, similar to what I have been riding. I have never had any knee problems, but by Sunday afternoon I felt like an old man.
I talked about this with my LBS. My theory was that the pedal threads were not perfectly aligned, causing my pedal spindle to be (very) slightly off-axis. Their theory is that the cranks were deflecting under load, causing the same problem: pedal axis to be off horizontal when using strong force. Same symptoms, different cause. I agreed with the LBS that the pain was sharper under heavy load, especially climbing.
My question is this: Has anyone else experienced this level of flex in their carbon cranks? It is very slight, but after 15+ years of riding my knees know a good rotation when they feel it.
For what it's worth, the pain was somewhat alleviated by kicking my heels out slightly. I am going to try realigning my cleats by a degree or so and see if this helps. Footbeds might be another option, but I would probably just go back to my old (Record) cranks.
Thanks for your comments.