I've also been having knee issues riding the fixed(I'm 32, btw). I found that it helps when I only resist on the up-stroke of the pedal and not the down stroke. Also, getting your bike fit perfect or as close as possible to perfect really helped with my knee issues.

I went to my Dr about my right knee, which was popping and stiff sometimes. Xrays showed nothing was wrong with the knee. Personally, I think it might have been from an old injury when I was about 15 years old and the high gear I was running (52x18)exacerbated the problem. My fix got stolen last week(Grrr!) and I haven't really been riding except for a group chopper type cruise on the weekend.

My knees are kinda sore and I can feel my quads withering away. Luckily, I get to pick up my new Kona Paddywagon tomorrow so I can get back on that horse.

To the Op: Dude! Go to the Dr! Its only money and replacement knees suck, or so I hear.