First off, spinning a low gear is not going to cause knee problems. In fact, it often helps aleviate them. As to pushing a higher gear, maybe, but it could just as easily be a technique or positioning issue, or it could be an unrelated physiological problem that manifests itself when putting a high load on the joint. When you say climbing, is it in the saddle or out of the saddle? Do you use foot retention, and if so what type, clips / straps or clipless? Have you ever had a pro bike fit? Anyways, there are a multitude of possibilities here.