Thanks Feuer CC I appreciate your help

You've got it right. I also asked the physio and knee surgeon about it and the basic idea was that I did damage the cartilage enough to let too much pressure through to the knee bone and give myself a bruised bone.

The MRI results are a bit misleading since they can tell how much the cartilage has narrowed if at all but it can still be damaged enough to not protect the knee well. They say the only way to really check just how damaged the cartilage is is with an arthroscopy but I probably won't need one (fingers crossed).

The freaky thing is that you don't have pain receptors in your cartilage apparently so by the time I started feeling knee pain I had already done the damage because it was my bone being bruised! I was just happily running along messing myself up!