Here's a "for what it's worth" from a former runner turned Pilates trainer...
Not everyone has the bio-mechanical efficiency to run for life. Minor structural imbalances are magnified by the act of running. Try to get an assessment from a physician who specializes in sports injuries.
Cycling (stationary or the "real thing") provides a decent cardio workout and is actually good for the knees.
Try to re-educate the body as to how it uses the knee. If every time you straighten your leg you simply flex the quads, the knee joint will jam a bit, exacerbating whatever problem that exists. This is normal for most people, but there is a better way...
Instead of initiating with your quads, think about moving your heel and sitz bones away in opposite directions. This produces a lengthening contraction in the hamstrings which opens the knee joint. Of course you use the quads (you can't not use them), but you begin with the back of the leg.
Translated to walking, this means pushing off one foot to lengthen up out of the hip of the reaching leg. Sitz bone lifts, heel reaches away, and the knee opens.
Hope that helps,
Tom
http://www.pilatesconnections.com
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