Maltracking can cause loads of pain, you have my sympathy. However, if your doctor can't find anything wrong with the underlying anatomy (assuming he is correct), it may be muscle imbalances which are pulling things unevenly. The fact you say that something seems tight on the outside (lateral side) is what leads me to say this, as well as the fact that ITB stretches give some relief.
I know that PT can be really difficult to stick with in a meaningful way. If it hurts, and you don't see results, it basically impossible to stick with! I wonder if maybe you need to vary what you're doing a bit. In particular, I think trigger points in your IT band may be an issue.
On stretching the IT band
- what method are you using? My physio wanted me to do it like this:
However, I struggled because my muscles were so weak, and the best I could manage frequently was more like this:
This helped a little bit, but I still had plenty of pain. As it turns out, I had more serious issues with bones being poorly arranged and causing the maltracking, rather than just muscle imbalances. However, I did want to learn more about why I found it so difficult to lengthen the IT band, when its tightness was making things even
I started trying some different types of stretches. The first proper relief I got from pain (whilst I was awaiting surgery to deal with my bone issues), was using a foam roller. It was really effective at loosening the IT band and getting me walking better.
I didn't really understand why this worked so much better than just stretching, until I understood about trigger points. I found that my abnormal anatomy and subsequent poor walking habits had set up chains of trigger points which caused the tight IT band and plenty of other problems. I only realised how big the problem was when I had surgery on one leg, and could witness the difference between a fixed leg, and one which still had chains of trigger points (which I could only ever get rid of temporarily because of the bone issues).
Trigger points develop in muscles as tight little points of contraction, which then leave the rest of that muscle stretched very thinly. This can cause pain in the joints which that muscle attaches to. It also makes it very difficult to strengthen that muscle, because it's pulled tight and can't contract properly. Just stretching won't get rid of trigger points - you need to massage them to get rid of the chemicals causing the localised contraction. You could have trigger points in your quads and along your IT band, which would then be tight and pulling on your kneecap. A foam roller is imprecise but nonetheless an excellent start at getting rid of them. For better understanding, and more precise work to get rid of them, this book is great.http://books.google.co.uk/books/about/The_Trigger_Point_Therapy_Workbook.html?id=IYqqY5Ae_VoC
Just to offer you some hope - in between the two surgeries I needed to deal with my more substantial issues, I was in loads of pain from this problem. I found a great massage therapist who specialised in trigger point therapy, and within three weeks of her working on my bad leg, I was walking without pain for the first time in years. It made a phenomenal difference, although it took a bit of studying that book to understand what was going on.
Before the pain, were you doing any exercise like running? Or did you have any injuries?