Just to further muddy the water in this debate, I had a serious ankle injury to my right ankle (same side as the knee problem), which stopped me from training for 6 months. The ankle doesn't hurt atm, but the foot is now tilted to the outside when standing flat footed, so that more of the weight is carried on the outside of the foot relative to the non-fucked ankle. Not sure there is any way to fix this, but ankle exercises are part of my standard warmup now. I also had hip-flexor problems on that side last fall.
Regarding the VM/VL debate, I noticed that when releasing the VL on either a foam roller or using a tennis ball results in immediate relief from my knee pain, leading me to give favour to a VM/VL balance issue as being a cuplrit in the pain itself.
I'm quite sure there could be several issues for PFS, as its a pretty broad term for knee pain.