I put nearly 2000 miles on my bike before I noticed any knee issues, however once they started they quickly got bad, and I was forced off the bike and in the doctors office. Was told to take 4 weeks off, and prescribed 4 weeks of physical therapy. The physical therapy did wonders for my range of motion, but nothing for my knee.
I went to the Bike Barn custom fit studio here in Houston and spent 4 hours getting fit. That evening I rode 25 miles, 45 the next day, and 180 miles over the weekend with no knee issues. I went from not being able to ride one hour without pain that would force me off the bike, to riding 250 with no complications. Additionally, I picked up a little speed and endurance with the increased efficiency.
I made a short you tube clip to share with some friends, I will
link it here for you. In the head on shot you can see my knees making triangles, not to mention my arms are so locked out I have no shoulders. The biggest affect in straightening the knees actually came from shoe inserts. Anyway, get a good bike fit, its worth every penny.