Is it just one foot that is turned in?
Couple of things spring to mind...
*If only one leg is pronated and internally rotated may be compensatory from leg length discrepancy
*Check out hip quadrant..have found a couple of patients where congenital hip problem was missed and this was causing altered biomechanics
*Make sure neuro is fully assessed...had a couple of missed mild cerebral palsy patients and sharko marie tooth (I know this is spelt wrong)...basically some mild neuro and more serious one can cause similar presentation
*Obviously also check out past history thoroughly...including falls out of trees etc as a child, as had a couple of growth plate type compression injuries that have altered mechanics of knee