I would check to make sure it is the hamstrings and not the plantarflexors. Lay the pt prone and see if the knee goes straight. If not I would take a closer look at gastroc etc length (ie dorsiflexion ROM). If the pt has been walking with a flexed knee for basically a year as you stated, there are going to be posterior joint capsule contractures. Check the capsule for tightness comparable to the other side. Add joint mobs if it is tight. Contractures of that time period also need several hours of low-load prolonged stretches. I will try and find the article but it was along the lines of 2-3 hours slowly building up of course to obtain changes that stay.