Hamstring strain recovery problems

I strained a hamstring in late April. Once the strain was confirmed by a doctor I was sent for physical therapy and I've been in PT for over 2 months now. They've treated it with ultrasound, electric stim, extensive soft tissue work, deep tissue massage, etc. All workouts were stopped until my therapist felt it was safe to assume some light exercise, and even then it was mainly spinning on a stationary bike just to increase the circulation in the leg and hopefully speed the healing process. I eventually progressed to the point that 2 weeks ago we started the process of re-strengthening the muscle.

Here's the problem though...I have a desk job and the hours of sitting keep causing constant aching and feeling's of "pressure" on the entire hamstring. These feelings eventually go away after I'm up and about. In fact I'm now able to do a decent hamstring workout, ride the stationary bike a little more aggressively, even jogged 12 minutes on the treadmill last weekend...so there is progress, but given that I can't sit at my desk or drive a car for an extended period of time without noticeable discomfort concerns me. I'm not sure if this is typical of this type of injury, if I'm just impatient, or just a slow healer. Anyone encounter similar issues on the road to recovery? I've never had a hamstring issue....maybe this is normal, I don't know, but any thoughts would be appreciated.