Also, make sure you're spinning in easy gears. I know its harder to do in the wind but a higher cadence is less stress on the knees.

Another thought, crankarm length. Are your using the correct length? I use 165mm on my road bikes and had 170's on my mtn bike. I noticed irritation with my knees with the longer cranks (I also have chrondomalicia) so I put 165's on my mtn bikes.