There are a lot of muscles besides the hamstrings that attach to the pelvis and can therefore alter posture and cause back stiffness or pain. In addition, how can you know for sure that your symptoms aren't related to your herniated disc? Unless you had some kind of traumatic accident that caused your disc herniation, you likely had some kind of imbalance that predisposed you to the herniation, and unless you worked with a great therapist, chances are that the imbalance may still be hanging around.
I would spend some time with The Trigger Point Therapy Workbook by Clair Davies. Aside from possibly resolving your stiffness, it will help you identify muscles that are being overused. Having a massage on a regular basis would be a good idea as well. In addition, I would get educated on the specifics of neutral spine posture and make it a big part of your training to develop the strength and endurance to maintain this posture during various exercises.
Hope that helps, good luck!