DR - sounds pateller (big word for kneecap), in my case chondromalacia patallae probably from too much cycling too sooon rather than running, but has stopped the running for the moment.
Assuming it's that, checkout: http://www.drkiper.com/articles/runners%5Fknee.html and http://www.womenfitness.net/chondromalacia.htm, or for knee stuff generally : http://www.kneeguru.co.uk/
Problem I've found in being a runner, and more recently cyclist/triathlete, is the medics stop listening at 'runner' and assume it's all down to that, no any other sporting or non-sporting reason. Check out a few web sites to see common (or un-common) causes/treatment, as there's always several, and have a better dialogue with your gp/physio.
good luck with it
