Grinding in Knees, sharp pain, parkour

Background information...
I’m almost 18, male, 83kg, 6ft 3, eat very healthily, very athletic and I've been self-taught trampolinist for 5 years and I've been learning parkour for just over 1 year. For most of that I was quite reckless; unaware of proper conditioning etc. I did do a lot of muscles exercises but little stretching; I had strong legs but little flexibility which I know can cause problems. I've taken omega 3 and vitamin D3 (good for joints) for the past year. For the past month (when my knee grinding started) I've been stretching several times a day and now I would consider myself pretty flexible, especially my legs. A problem I still have is I’m a little flat footed when running but I never considered it much of a problem, when training I always land on the balls of my feet etc.


So the initial problem was the grinding sound when bending my legs further than 90 degrees, the sound only comes when pressure is on my leg so if I raise my leg in the air the sound is not there, but rubbing is still felt on the joint when bending. If I move my knees slowly side to side when sitting I can feel (placing my hand on the joint) rubbing, like bone on bone.


A few weeks after noticing this I went to see a specialist (full movement checkup and a X-ray), who surprisingly said there was nothing wrong with my knees and that the grinding should be ignored, and that I just need to increase my flexibility.


I increased my stretching even more but the problem still persisted, not convinced I ordered Glucosamine sulphate and Chondroitin supplements (500mg and 100mg) I've have 3/4 of these a day for the past 2 weeks (the effects have not yet been noticed; need to give it a month). These are supplements to repair and hydrate cartilage; all natural.


My knees haven't got any better still, over the past few days I've started getting moderate sharp pains in the morning, lasting 2-4 seconds. These occur randomly every couple of minutes after I wake up and slowly fade away later in the morning. My knees feel a little stiff when not moving but after warming up I have no problems when training.


Issues I have considered - chondromalacia, knee arthritis, runners knee, jumpers knee, bad knee alignment
a few other things...
for the past few months I have trained lightly and conditioned (no big jumps)
I have been using excerises which apparently help bad knees
I control all my parkour falls (rolls, correct weight distribution)
Im competing in Miami in a 3/4 months for Parkulture so I need to get this fixed asap (traveling from England)
Please help... too much stress for a 17 year old.
Im going back to the doctor soon
I drink a lot of ginger tea (anti inflammatory) which could mask damage,


Thankyou (me training - http://www.youtube.com/watch?v=e0FqSJ24H… Im the tall one)