Muscle Imbalance

Has anyone had an injury due to muscle imbalance? I have had issues with both my Achilles and Patella tendons this year, and when I was getting stretched by one of the volunteer trainers after a race, she told me it was because my quads and hamstrings were out of balance, with my quads being far stronger, which was causing my knee joints to tighten up. For most of the season, I had been concentrating only on s/b/r, while I used to weight train fairly often, especially during the winter.

Just recently, my patella has really been flaring up to the point where I can't run; thankfully this happened 20 min AFTER I crossed the finish line at the Chicago tri - walking and stairs have been tough this week. So I have gone back to the gym and am starting to do hamstring isolation exercises, along with hip abductors, and leg press (high reps, low weight on the latter). It's still a little sore, but I definitely felt good immediately after the workout.

I have already seen my doctor, who confirmed that I  haven't torn anything and suggested I take NSAIDs and RICE and to come back to him if it doesn't get better and we can talk about steroid injection.

Do you think working on hamstring strength should help the problem? Is there anything else I should be doing? I suppose I could ask my doctor for a rehab referral, but schedule is already pretty tight as it is...