ITBS also flares once knee bend is past 30 degrees in a squatting motion.

Having your feet pointed inward or outward doesn't just affect knee alignment but also which of the contracting and stabilizing muscles fire more.

I read something on lack of float (plus improper cleat angle position) where feeling the "need" to rotate your heel somewhere the cleat position won't allow can strain the biceps femoris tendons, which attach at the head of the fibula. So there, float may be the problem. But its' still not the LCL, though over time, you can strain the knee.

What kind of pedals do you have? Do you have any new calluses on your feet, such as under your 5th metatarsal? Do your knees track straight (with someone watching in front of you) or do they wobble?

Of course the greatest strains on the biceps femoris are caused by saddle too high and/or too far back. Have you evaluated whether your knee is over the pedal spindle (or how far off it is)? Do you tend to be a little short in the femurs?