Knee problems are very common with breaststoke swimmers. Often the underlaying causes are misdiagnosed, unless you see a sport medicine person who has experience with swimming/training related injuries.
I have knee problems from years of over training (swimming AAU, high school, college and now masters). After seeing several doctors (in college and beyond), I finally got a more believable diagnosis that explained all the symptoms. Most sports knee injuries are from single-event trama and will damage the patella, so that is what the look at first. Swimming injuries are from long-term overuse and may not directly impact the patella. Instead, you may have elongated the tendon and ligaments on the interior of your knees. The elongation will not hold the knee together, creating delocalized issues.
There are some good exercises to strengthen the muscles around the knee, but the best long term solution for me has been to reduce (but not eliminate) the amount of breaststroke in workouts. I still successfully compete in breaststoke events with limited knee pain. At least one doctor suggested surgery to shorten the tendons/ligaments, but I would rather stop swimming breastroke altogether before having the surgery.
Bottomline: See a Sport Medicine doctor with experience with swimming injuries to confirm your initial diagnoses.
Anthony Thompson, Missouri Valley Masters (Kansas City)