Interesting. This is something ill bring up with my physiotherapist. I will ask her to check my hamstring strength to see if there is any imbalance. My previous physiotherapist had told me my hamstrings were weak. Maybe its something to focus on by strengthening it and see if there is any progress. 

Was your issue only in 1 knee? Cause I have a hard time imagining how a hamstring weakness will cause unilateral knee pain unless the hamstring weakness is on one side.