Hmm, can`t help thinking you may have started out too hard, expecting too much from your knees.
http://www.tri247.com/article_2670.html

http://www.bikefitting.com/English/S...roduction.aspx

http://www.peterwhitecycles.com/fitting.htm

http://sheldonbrown.com/frame-sizing.html

http://www.rivbike.com/kb_results.asp?cat=23

The film made me think your saddle is high, too high.

I support fietsbobs suggestion on finding somebody that can "read" your body that ia also into cycling. they must be out there. Maybe as you say stay away from peopel who would only try to sell you a new bike.