I'm not a doctor and don't even play one on TV, but I have a wild conjecture with a single data point to support it. When I first started cycling back in the 1970's I rode a lot of miles without toe clips. My quads got very strong but my hamstrings didn't. After some time my knees ached all the time unless I was riding and then they felt fine. My hypothesis was that the imbalance in forces on the knee joint at rest was causing the ache. After getting toe clips and straps the knee ache went away pretty quickly. Perhaps there is something in your pedaling style that is causing one set of muscles to get stronger than its opposing set? Just a thought and probably worth exactly what you paid for it.
