http://www.cptips.com/knee.htm

Pay special attention to the Anterior and Lateral sections.

Sounds more like an overuse injury. When you ride for 5-7 hours with your legs constantly moving all those muscles go through fatigue cycles and since the knee is a joint stabilized by muscles when you get fatigued the moving surface relationships start to degrade and you get irritation from Chondromalacia.

Generally, long distance riders prefer saddle and cleat setback to the max. For fixed riding this can compromise spinning ability but it does generally improve the comfort level during lengthy rides. Long-distance fixed-specialist and former contributor to this forum, Paul Rozelle, appears to ride a fixed gear with no knee pain. So it's definitely doable, the combination of fitness, fit and physiology are the main factors you need to think about.

http://www.thebicyclestory.com/2011/...ventoux-rides/

Note the setback of the saddle.

ETA: LOL. Now I remember you. Apparently the point of riding fixed it to destroy your knees. Riding with a brake would definitely help your condition.