Yeah, I don't really want to switch to single speed...the continuous flow and connected feeling I get with the fixed kinda overrides all of the discomfort. To be entirely honest, just one of my knees really acts like a jerk, and its not inside the knee, its the ligaments below it that start complaining when I get on with the high spinning. It only really starts getting tetchy when I do 15-20 miles in a day. I've been out training just about everyday on a 10 miler for the last three weeks without a single pain--I attribute it to stretching after my ride.
I should probably try different gear ratios--it may be the lower teeth and spinning that's causing my problem..