When you are stretching your hamstring, are you dorsiflexing or plantarflexing your ankle? If you are dorsiflexing, it is likely that you just have a very tight posterior fascial line, spanning from your plantar fascia, up through your calf, hamstrings, and into your glute (and possibly even higher).
There is a slight chance that there could be a disc involvement, but more than likely it is just soft tissue.
I'd just look at the soft tissue quality of the plantar fascia, calves, hamstrings, and glutes. Roll all of those structures out and work on good ankle and hip mobility.