I went to see a different phyzz today. She examined my knee thoroughly and asked lots of questions.
There is nothing seriously wrong - no meniscus problems. Probably the medial ligament causing problems something like this.
She has advised me to take a couple of weeks off running to try and normalise the strength in the leg. So lots of exercises - half squats, leg press, balancing on the bosu together with swimming and cycling - but don't get any funny ideas.
I really want to get this right and need to focus on doing these exercises for the next few weeks while I have time.