Hi Jonny,
I'm not a physio, but last year I had some chronic knee problems, which I eventually got sorted.
I have some useful sites that you might want to take a look at. Copy and paste these lot into you browser.
http://orthopedics.about.com/cs/patelladisorders/a/chondromalacia.htm
http://www.mckinley.uiuc.edu/Handouts/overusekneeinjuries/overusekneeinjuries.htm
http://www.kneeguru.co.uk/
http://www.knee1.com/care/condition20.cfm/98
All I will say, is I hope your physio is good. I had some shocking advice last year, until I saw sense and went back to my tried and trusted physio, who I worked with for a while and got my problem dealt with.
If it is runners knee or Chondromalacia Patella as it's also known, then it can be sorted, mainly through corrective exercises that involve strengthening the quad region.
In the end I wasn't suffering from this, but I remember my physio telling me all sorts about knee injuries during my treatment, and he mentioned runners knee.
Give some of these sites a go first, and go back to your physio, and work with them to get the correct diagnosis. It's unlikely to be an overnight fix though.
Best of luck!