I think, fingers crossed, that the knee issue I have been experiencing has quietened down.
Essentially I was getting a sore knee after running or riding hard up some tough hills.
I noticed that my knee cap would click from time to time which I believe is the knee cap not tracking correctly as you bend the knee. I was also informed that one hip is higher than the other, probably an imbalance caused by desk job.
So I tried some off the shelf orthotics for when I'm just walking around (not riding or running) and after 3 weeks I reckon they are doing the trick. Got a bit of lower leg pain at first as bits n pieces adjusted but all seems pretty good now.
Will look soon at upping the pace on my 5km runs and then upping the distance, gonna take it real slow coz I aint no spring chicken.