Dunno if this makes any sense but here goes - ask the physio/podiatrist...
I used to get knee pain due to being an overpronator, but then got antipronation shoes. In my case this was partly caused by a problem near the top of my leg, whichmeant the feet had to roll in otherwise it was uncomfortable, which triggered the pain in the knees. Since the anti pronation shoes reduced the roll in, the knee pain stopped - but this left me back with the original cause of the roll in at the top of the legs.
It was a bit more complex than this as part of the over pronation was also due to feet problems, but that's the gist of it - curing a problem in one place may just transfer the problem to elsewhere. I would imagine a good physio would take all this into account and go for an overall broad view rather than just a localised one.
Hope that made sense!