I agree with the physio just wanting to get you out the door. I was seeing an actual sports physio via my health insurance who wasn't working to get me better but rather getting me back out running (there is a difference). Take a look at therunningschool.co.uk i've had a couple of sessions with them and they are brilliant
I started running with normal trainers but after about week 5 I went to find out what was most suitable and did a gait test. I overpronate and bought suitable footwear. The issue first happened after about 13 weeks. Interestingly, the times I've run on the treadmill I was in a much warmer climate. I do stretch and walk to warm up when at home. The physio (NHS) didn't seems to be interested in looking at it further and suggested I give up and swim or cycle. I have no interest in either. I suspect that the unwillingness is probably down to cost of further investigation so my best option now might be a private referral.
I completed the c25k in the Autumn but had to stop running due to lower back and hip pain . Really sad to have had to give up but couldn't risk a long term injury
In answer to luketelfer -delivery was good and kept me informed of delivery on the day of delivery. The guys carried the box around the back of my house and into a conservatory, however I would suggest you ask about delivery upstairs as these are very heavy and carrying up 3 flight of stairs would be quite a challenge.
Its most likely an issue with your running gait. I have been running for year now and i've had knee issues for the past 2. i recently had gait retraining and now no longer have the knee issues.