I dealt with Pes Anserine Bursitis for a few years but it's been totally under control for the past 18 months or so. When it was flared up I was running 40-50 miles/week. Now I've been running 55-65 miles/week consistently and it hasn't returned.
In my case I think it was ultimately caused by a stiff ankle. My knee would have to compensate for the lack of ankle mobility. At its worst, I'd have very sharp pain at the medial knee with any type of terminal knee extension. Touching my toes would be painful. Single-leg supine bridge on the affected leg would be REALLY painful, and I couldn't hold it for more than a few seconds due to the pain. That was my benchmark move to test if things were improving -- could I hold a single-leg supine bridge without sharp medial knee pain?
Some ideas...
Check you ankle mobility. I do this type of ankle mob almost daily:
http://www.crossfitinvictus.com/wp-content/uploads/2015/07/IMG_2339-e1435763521810-768x1024.jpg
Ask your physio to mobilize your ankle(s) if you find issues with range of motion.
I do "Whartons" (rope stretching) regularly. In particular, the bent-leg and straight-leg hamstring stretches. When my pes anserine bursitis was bad, these would be a little painful for the first few reps, but as it warmed up the pain would subside a bit.
https://www.youtube.com/watch?v=3QVwqy-PiGo
Along the way I really improved my glute medius strength which helps with hip stability (minimized hip drop and extra loading on medial knee). Ask your physio for some glute medius exercises (e.g., clamshells w/theraband, straight-leg side steps with theraband, etc., etc.). Here are some other examples:
https://www.youtube.com/watch?v=85B1dfmgxrg
I had regular ASTYM on the three related muscles (SGT = sartorius, gracilis , semitendinosus), also the gastroc and soleus, maybe twice a week for 4-5 weeks.
I had some cold laser and EPAT treatment on the knee area when it was at its absolute worst, but I'm not sure how effective that was. That was a last-ditch effort, but I ended up DNS'ing a marathon due to it.
Hope this is helpful. Good luck!