knee problems due to breastroke

I'm new to the forums here, but I'm having an issue that I was wondering if any other swimmers had come across/have tips for... I've been swimming since I was very young, used to swim on teams but don't anymore. Now, I just swim laps as a workout...it also helps me to relax and take my mind off things. Throughout my years of swimming, I never had any sport-related injuries that affected my swimming...until recently. This past summer, I began having pain in my knee when swimming, particularly when swimming breaststroke. I went in to see a physical therapist, who determined that the problem was patellar tracking disorder...basically, my kneecap in my right knee doesn't always move quite smootly and straight in the socket. She thought it was probably caused by the breastroke kick. I've been doing physical therapy exercises to strengthen my inner thigh muscles, some stretching, etc. It's helped, but I still haven't been able to get back to where I was before I began having problems. My question is, has anyone else had a problem similar to this, and what's your advice? Currently, I only swim freestyle and backstroke during my workouts, with some breastroke every once in a while. I don't compete, or plan to ever again, really, but I want to be able to continue swimming laps without making my knee worse (I'm currently in college, by the way). I usually swim between 2000 and 2500 meters during a typical workout lasting about an hour...I don't swim extremely fast, but I like to be able to feel like I'm really using my muscles and getting a good workout. Any advice is appreciated...I've been searching for information on this for a while now, and haven't had much luck, so I thought I'd try asking here...thanks!