Yea, I was going to say that you are probably not using correct technique as well, but you said you had been training for 3 years.....
You DO NOT make contact with the knee itself. HELL NO that'll mess you up. The knee bone (patella) is a free floating bone held in by ligaments and tendons, has some smooth cartilage and fluid around it. You are striking with the area just above it.
If you look at an entire human skeleton you will notice that the end of the femur (thigh bone) just above the knee cap is a HUGE bone that looks like a club. Compared to the rest of the skeleton, it's the part you would take a look at and figure out fists, shins, and elbows, it looks most deadly... I'm guessing that you either have been throwing bad knees for 3 years or you have a medical problem and should see a Doc.
And yes, we ARE talking about straight knees. The knee cap is weak, it's like kicking with your foot instead of your shin.. BAD.