Hamstring pain

Hi All...wondering if you can help me, I'm recovering from knee injury and gradually getting back into running. I seem to be picking up strains and niggles along the way but I assume that's all part of getting my fitness back. Recently I've been getting some pain in my right hamstring but I can't feel it when running/stretching, only afterwards when resting. Any ideas what it could be? Surely a strain would be painful when the muscle is in use? I've had a sports massage incase it was a knot but the ache is still there? Please help!
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