If you are still having troubles that impact your daily life after all this time, and if the tests show nothing, I would think it would be appropriate to have a diagnostic arthroscopy on your worst knee. I had surgery and was unable to rehab completely due to pain and swelling. After five months of tests and PT, nothing seemed to be wrong according to MRI's etc, but when my surgeon did a scope he found the problem (scar tissue) right away. Now, even though I'm not able to walk properly and we know what the problem is, it does not show up on any MRI or other imaging tests.
Sounds like you might need a new doctor, one who specifically specializes in patello-femoral problems. Try checking out the list of knee specialists on this page for one near you.
Good luck.
Heather