Had a similar pain during the same, turned out to be overly tight anterior leg muscles. Try this:

1) Pay Attention to exercise form, and other mobility aspects above and below the knee.

http://www.mobilitywod.com/2013/07/pro-episode-31-user-request-friday-live-from-the-games-patellar-tendonitis/

2) Smash your quads & hip flexors (and/or ITB & adductors if need be). Spend 8:00 per leg, twice a day.

Correct Quad Smash Technique:
http://www.youtube.com/watch?feature=player_embedded&v=5nlarY4AdQw

Barbell Quad Smash:
http://www.youtube.com/watch?feature=player_embedded&v=c57xVyqTEjw

3) Couch/wall stretch like it’s your job. I’m talking like at least 3 times per day, at 2:00 per leg (6:00 per leg / per day). This is the most important in conjunction with #1.*** If this is painful, your anterior leg is too tight.

http://www.youtube.com/watch?feature=player_embedded&v=-ZX1QMTdAC4

4) Smash and stretch your calves – make sure you have full ankle range of motion. Also, anterior tibialis: use a tennis ball, or lax ball and start to “peel” it off your tibia. Clean up the fascia right below the knee.

http://www.youtube.com/watch?feature=player_embedded&v=fCFlfgCqpK8

5) Voodoo band your high hip, mid quad, suprapellar pouch, and high calf / right below your patella. Perform squats (good form) and calf raises / stretches while in the bands for ~ 20 reps. Feed you knee joint some slack by voodooing above and below the knee.

1. http://www.youtube.com/watch?feature=player_embedded&v=-RYMV0salw8

2. http://www.youtube.com/watch?feature=player_embedded&v=JVRTnKUgARA

How To Make Your Own Voodoo Bands:

http://glennpendlay.wordpress.com/2012/02/17/got-tendonitis/

I don’t like the rumble roller that much. I think it, and lacrosse balls have too small of surface area for quads. I’d try something harder, with adequate surface area such as a PVC pipe roller or a softball.

Check your minerals

http://www.ivillage.com/chicken-soup-new-pre-workout-electrolyte-drink/4-a-122678

4) You mention couch wall/stress each leg. My problematic knee is the right one, although I have tight IT band/quad/hip flexor complex on both sides. Should I still do both legs, or focus more on my right leg?

Ideally as a coach, I would tell you to do both equally. When I was in full mob-mode, I probably paid 70% attention to the bad one and 30% to the okay one. As things eased up, I even them out. Don’t neglect the other one, it could end up like the other one if you don’t! But I’m not gonna lie, couch stretching like 3-5 times a day sucks, it’s not fun. That’s probably why I didn’t want to double it.

5) I am not fimiliar with voodoo banding the high hip, mid quad, and high calf. I have seen one of kellies videos were he vodoo bands somones suprapatellor pouch with a half lacross ball under the band, and makes him do squats. What will voodoo banding those areas you mention do? And If I voodoo band do you suggest to have half a lacrosse ball under the band? Is their a video that shoes voodoo beanding the hi hip, mid quad, and high calf while performing squats. I checked all the videos you posted Kaitlin. Maybe I missed it.

Voodoo flossing helps restore sliding tissues, and also helps flush out joints as well as get some new blood to them. Above the knee often gets matted down with all the common muscle insertions. I’ll post some videos here in a little.

6) All the exercises/stretches kelly performs with some type of band, around the high hip and gluteal fold area while stretching the hip flexor/high quad complex. Is that with a voodoo band? You did not mention performing those exercises, did you not perform them,? Are those capsule stretches?

That is just a jump stretch band. It’s not a bad idea to throw those in when you can. It can be awkward to set up though. I only used banded distractions about 10% of the time.

After I get all the links to videos, I’ll resubmit my 1-5 to help make things clearer.

I was in a similar situation recently. Long story short, at the beginning of June I began getting this anterior knee pain, right above the knee. I would wake up in the morning with my knee feeling stiff, like it was under constant pressure. The pain worsened after prolonged periods of sitting, and seemed to hurt most when my knee was in more flexion. The pain would die down to around a 1-2/10 after a really good warmup / session of foam rolling and stretching. Despite being a trainer myself, I let this go on for almost 5 months. Training for the AF > focusing solid mobility (bad).  Out of frustration I visited a Physio who told me to do quarter squats off of a phone book, and ice it. $30 wastedddd.

I’m going to say I don’t believe in VMO imbalances causing this kind of knee pain, and that’s an outdated theory, and anyone prescribing quarter squats and TKE’s is probably wasting your money. 

I finally decided to sack up and research the hell out of the situation and commit to rehab 100%.

The problem with your approach is that you said you do physio exercises only 3 days a week, but 2-3 hours long. You need to do them maybe max 1 hour, but EVERYDAY, twice a day. If your situation is like mine, your tight quads, hip flexors, and calves are all pulling on your knee either directly, or indirectly through fascia. After loosening those up, my “weak glute” started firing just as strong as the unharmed side.

This is how I kicked what would have been a never ending cycle of misdiagnoses from doctors for years:

1) Smash your quads, ITB, and hip flexors. Specifically, your rectus femoris. Show no mercy; you need to drop the foam roller and start smashing that with a barbell and a softball. Spend 8:00 per leg, twice a day.

2) Couch/wall stretch like it’s your job. I’m talking like at least 3 times per day, at 2:00 per leg (6:00 per leg / per day). This is the most important in conjunction with #1.***

3) Voodoo band your high hip, mid quad, suprapellar pouch, and high calf / right below your patella. Perform squats (good form) and calf raises / stretches while in the bands for ~ 20 reps.

4) Smash and stretch your calves.

5) Smash your anterior tibialis; use a tennis ball, or lax ball and start to “peel” it off your tibia.

Assuming your situation is similar, commit to this for a couple of weeks and you’ll just notice one day that you’re pain free. Unfortunately, I don’t have any time tonight to hunt down links for those 5 things, but Kaitlin is usually a wizard when it comes to links, so she may beat me to it sometime this weekend. Good luck!