are you referring to "tracking" as your knees staying put, not wobbling in and out towards/away from the top tube as you pedal?
I had my fit done by one of the best guys on the east coast. He applies physical therapy methods, and other anatomically based methods to assess the athlete before the fit even takes place.
something he has me doing before every ride is popping your hips. basically your hips sometimes come out of alignment in the socket thus creating leg length discrepancies. try this:
lay on your back on flat ground with your knees up at 45 degrees, feet on the ground, butt/back/head on the ground as well. do 3 bridges, pushing your pelvic area as high as possible, hold for like, 5-8 seconds. once you do that, stay in the same position, have a football, or solid object about the width of your knees when you are on the bike. (could be a ball, football, foam roller,etc). Promptly after your 3 bridges, put the object inbetween the knees and squeeze inward as hard as you can, 3 times. you will probably hear a crack, and this means that your hips have aligned. next same position, but lift your (shorter) leg pull your knee into your chest and hold it there with your arms/hands. push upward as hard as possible 3 times. complete.
you basically intitially have to figure out which leg is the problem leg. you can do this by locating the trocantor(spelling?) and looking in the mirror with a finger on each side marking the height. whichever is lower is the leg you need to align in the above procedure. it may work for you.