Last summer I didn't realize that my seat post clamp had allowed my saddle to drop. I was on a long tour(cross country) and thought I might have to throw in the towel...... My left knee was hurting like heck right on the knee cap. After days and days of this I figured out what had happened. Pain went away pretty soon after I got everything back to normal.

Not saying that is what happened..... but look over all your settings very close. I was amazed how much pain I got from a saddle being to low.