knee pain behind knee cap

I had allograft surgery for my torn ACL and was recovering way ahead of schedule.  After almost two months of PT, I was doing the Cybex machine, as usual, at PT (leg extensions and curls in one exercise -- sit up with ankle strapped and extend/kickout leg then pull ankle back in under you) when I realized that I had set the machine to allow me to FULLY extend my leg.  After doing 10 reps, I adjusted the machine back to only allow me to extend partially, like before.  I didn't feel any differently during those first 10 reps but by the end of all my sets, I knew something may have gotten tweeked.  Since then, my pain has intensified.  I have suspended PT (doctor's orders) and have to rest it.  Doc thinks it's petellar tendonitis but all my pain doesn't seem to point to just that.  I do feel pain below my knee cap and behind my knee when I go up and down the stairs, when I lay down and try to lift my straight leg from the ground up.  What worries me is that I also feel like somewhat has dug a blade behind my kneecap and there is something there 'in the way'!  Since that PT session, there is a new golf-ball sized (diameter, but not as puffy) swelling just above my kneecap -- it wasn't there for the first two months after surgery although my knee of course had some other swelling going on...normal.  The pain seems to be that of patellar tendonitis but more than that, I am worried because my knee wobbles again (but the doc says the ACL feels still intact) and that new pain cuts across my knee more on the back side or deeper inside, in addition to the under kneecap pain/burning.  What could this be??  It's been almost 4 weeks and no relief even after RICE and a prescription anti---inflammatory.