I can certainly relate to the 'behind the knee' pain. I've been having a love/hate relationship with the local medical community for the past 5 months to figure out what is wrong with my knee. My symptoms are as you describe. The worst pain is what they call 'movie goers' knee. That is where sitting with you knee at a 90 degree angle for a couple of hours is very uncomfortable. I haven't been able to trace it to a specific cause although I had a couple of spectacular yard sales on my MTB this spring.
So, I went to my regular doctor who said I may have bursitis (fluid on the knee) or PFS (patella femoral syndrome). Got put on Celebrex for a month to no avail. Went back and got some PT prescribed. Tried that for 4 weeks to repair the PFS. BTW, PFS is when your knee cap does not track correctly in the groove with you leg bones and starts to eat up cartilage. PT helped a little but not enough. Finally got a referral to an orthopedic surgeon (OS). He took some x-rays and came to this conclusion: The good news is I don't need surgery. The bad news is I don't need surgery. Although the PFS seemed to be gone, there seemed to be some roughed up cartilage under my knee cap that will wear itself down in a few months with repetitive, low impact exercise ... biking! Which may be what got me in this mess in the first place.
If you think PFS may be the culprit, do some exercises that will strengthen you inner quads: leg lifts, low-angle leg extensions, etc. Google search on patellar femoral syndrome will give lots of leads. Otherwise, the OS said stretch the hammies lots, and keep working the quads. Also a steady diet of ibuprofen and ice to help inflammation. I also got a pro bike fit and put some wedges under my pedal cleats to correct a pretty good pronation problem I have (like most people).
The reason I drag on about this is the OS said he figures most of the non-trauma induced injuries he sees are repetetive motion types, of which PFS is a large part.
Good luck with it!
BTW, my 'injury' helped me convince my wife I needed a new road bike: 1) to keep me from hurting myself again on my MTB 2) to fix the problem biking caused in the first place!
