In reply to JimR:
There's so much going on in a knee, and such varied trauma caused by running, that it's very hard to give an interweb diagnosis beyond guessing that you're irritating some bit of soft tissue (obviously...).
Quite often chronic soft tissue injury/pain (ie caused by repeated stuff like running) is caused by 'wearing out' the tissue faster than it can be bothered to repair. Sometimes some vigorous and burly movement like a rockover can help to encourage healing by giving it some more straightforward knocking around. It could also just be that climbing and moves like rockovers are helping to stretch out tight muscles/movements and therefore correcting something that is bothering your knee.
I've always found this stuff near impossible to target directly, but have made inroads in particular issues by doing a general regime of strength and movement exercise to tackle my imbalances and weaknesses. I needed a professional eye to point me in the right direction a few years ago, but it has stood me in good stead.