2 things for knee issues - spd's with lots of float.
Different types of exercise - sometimes the muscles around the knees can get overdeveloped in one area due to the amount of one single exercise you do - these overdeveloped ones then pull the joint out of shape. It's worth trying a gentle run on grass or a track or some leg exercises & stretches. Best advice is a physio who can identify if its muscular or joint/ligament related though.
Do see a PT if you have problems, but audition them carefully. The current state of the art - based on surfing pretty technical sports science articles after talking to a friend who had a leg muscle problem - says that stretching does not work for over-developed muscles. In fact, it's becoming increasing questionable whether it works for anything you should really care about:http://www.runnersworld.com/stretching/ ... t-injuries
Instead an up to date physio will probably have you doing strength work on the opposing muscle to the one that's over-developed and some **dynamic flexibility** work on the over-developed muscle itself.