In reply to Jonathan:
You might find it instructive to go a bit further afield than a physio. I'm going through something similar, but with my left calf, rather than my knees. I've done much as you've done - physio, podiatrist, foam roller, massage and so on, and things gets fixed up to a point and then it goes wrong again.
Last week I went to a sport doctor, who has suggested that the real problem is not with my calf but with my pelvis, which is misaligned, and this is causing uneven distribution of forces through my legs. So, there's a course of treatment to be undergone to realign the pelvis. The jury is still out - I haven't had the treatment, so I don't know if it's actually going to sort things out - but I'm certainly willing to believe that the root of the problems lies somewhere other than where the pain is.
If you can find a decent sports doctor, you might find it a useful exercise. It might be a bit more expensive than a trip to a physio or massage therapist, but as a running friend of mine pointed out, it's less than we'd spend on a pair of running shoes.