Yep the hamstring tendon graft nearly always causes hamstring problems for at least 12-18 months post the surgery. It is pretty basic 'blind' carpentry when harvesting the tendon and everyones anatomy and recuperation ability is different. That said I myself would rather than than a patella tendinitis following a graft from that region.

You are not alone in your issue. I see this more often than not which perhaps means the surgeons should look at the way they make the harvest. As for the muscle it sounds like it is reacting in a normal way to excessive leads placed upon it to soon.

Suggest working with a good remedial massage therapist and PT to work on a graded approach to your return to activity. This plan make take another 6 months. Of course if a scan has shown a problem in the tendon then perhaps a surgical investigation and clean up might be useful as well.

Good luck.