Get yourself some knee wraps, not the heavy duty kind, just some normal knee wraps. UGE has them on special for 35 bucks at the moment, get some and give your knees a little support until your body heals whatever it is that is going on. I have some knee wraps, I use them occasionally for squats, don't know why but I get a sore knee here and there, but the wraps take care of it no worries. I think it is more about keeping my knees warm as I don't wear them tight enough to affect my lift. Try some mate, they work wonders.
Graeme