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On recent cycle rides after a few hours of cycling the outer side of my right knee feels sore. I am think this down to lack of cycling, weight training and old cycle shoes or could be it be somthing else?
Try sitting on a table with your legs free to swing. Look at the way your feet (in cycling shoes) are - specifically the angles. Try to replicate the foot specific angle for the individual cleats - as Gastank says, it sounds like the way your legs are tracking. Easiest thing would be that your cleats could do with adjustment.
I had a similar issue and found that twisting one cleat out made a huge difference