Hi,
I am in a similar situation, so I feel your pain (literally). I'm 25 y/o male. I never had any knee problems in my 10 years of running and I even ran D1 cross country in college. I was diagnosed with runner's knee/patellar maltracking 7 months ago. I did PT for 4 months with no improvement. I got an MRI in that 4th month. The only problems that showed up were induration and stranding in my hoffa's fat pad and my suprapatellar fat pad (No evidence of chondromalacia). Diagnosis was confirmed as originally thought. My original OS said it must be patellar maltracking. Two weeks ago I finally got a second opinion. This OS told me I have cartilage damage on the back of my kneecap and wanted to schedule a scope to do a carticel biopsy. I was super surprised because the MRI report said in bold terms "NO EVIDENCE OF CHONDROMALACIA". However, I have read that MRI's aren't particularly accurate at discovering articular cartilage defects, so I have scheduled the scope for 2/18/15. I am hoping my doctor is wrong because cartilage damage on the back of the kneecap could mean I might never be able to run again, at least at a competitive level. If the cartilage damage is confirmed, I'm looking at a very serious Cartilage implantation surgery with a lengthy and difficult recovery. Long story short, you might want to get a second opinion and consider an MRI/scope if you haven't had one.