It seems like there is certainly an element of muscle imbalance going on with the relationship of the hamstrings and the lower back. If that were so the hamstrings stretches were along the right line but they would need to be combined with core stability exercises. It can be fairly common to have variances in kinetic control and muscle imbalances following surgeries on the knee.
I would also agree with violablue's other common problems and I feel that the symptoms seem more of a myofascial origin. Saying that I wouldn't rule out other sources as a proper assessment isn't really possible on here
Good luck
Chris