I am going through this at the moment. I raced cross this past season and logged in alot of miles last year. Here lately I have been having horrible knee pains in the same area. I have tried adjusting saddle height and position, adjusting horizontal pedal movement, switching saddles...nothing. I can normally get in about 10-20 miles and then the pain starts. For the next couple of days it is sore to the touch in that area and stiffens a bit if I sit down. Applying in force with my legs makes the pain worse.
For an answer, I have no clue. I have been trying to figure this out for a month now.