Hi Sarah, another relative newbie with a knee issue. I had my gait analysed (neutral) did the Couch to 5k in May-June 2011 and went on to run a half marathon in November 2011 - all with no problems, not even a blister. I developed a knee problem that I've had before on walking holidays, the one where it's excruciating to go downhill and down stairs but all other movement is pain-free. I started barefoot running in spring 2012 to try and sort the knee pain, but after a few months I started getting knee pain in the same knee but a different place.
From googling various anatomy pics, the pain is in the area of the tendon that attaches the vastus lateralis to the knee: about 1 inch above my knee cap to the outside of my thigh. I was continuing to run with this but eventually it was too painful to continue and I haven't run since September 2012. At first I only had this pain when I ran, but since about November I've been experiencing it on and off every day, while sitting, standing and walking. I went to a biomechanic clinic who said I needed an ultrasound to diagnose the soft tissue damage he could feel (he said he could feel a lump that might be a cyst), but my GP told me to take Ibuprofen for a week (it didn't help), sent me for x-rays (they came back normal) diagnosed "probable tendinitis" and suggested a steroid injection (if he's not 100% certain, he's not sticking a needle in my knee!).
I'm still in pain and don't know what to do next, and would really appreciate your advice - thank you.