Join Date: Feb 2008
Location: Oxnard, CA
Bikes: '08 Fuji Roubaix RC; '07 Schwinn Le Tour GS; '92 Diamond Back Ascent EX
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Could be several things. Seat could be too high. If your hips are rocking when you pedal, that's an indication you need to drop the seat a bit. Also, your seat should be far enough back so the front of your knee is above the ball of your foot when the pedal is at 3:00. Lastly, you should be in a gear where you are spinning the pedals not mashing them. As someone used to powering through things, this may be the problem. You should work to get your cadence up well over 60 RPM (95 is most comfortable for me) and spin away. Put less pressure on the pedal and therefore on your knees.
EDIT: Just noticed where you are from. Keeping your knees warm is also very important.