O knee problems, I feel your pain, it really takes a bite out of your confidence and training! Im gettin surgery on mine in a month, but ill only be out for about a month(or maybe less because im tough

) Icing them nightly has helped me alot, and chilling in my spa also helps.
Put your feet togethers standing straight up, bend your knees (not to much, just enough so you feel pressure on either your knee of quads). Now, with your weigt on your knees move your knees together in a circle for 15-20secounds, then switch directions. I do that after track 2 or 3 times then go ice. It was recomended to me by an ahtletic trainer, so if you want give it a go...its some crazy yoga or something.