Running

I think that may be it. One leg/knee is now much more supported than the other. Is it worth me putting the insoles in each shoe or is that more trouble than its worth and I should just leave it in the shoe which actually needs the support?

If the support is a recent addition. Chances are you will settle into an adjusted gait, and get used to it. Its the same sort of ache, beginners get because the legs arent used to running. Except you're not a beginner, so you put more km's on the leg, that is suddenly functioning slightly different. Subtle things make a difference over distance.

I cant advise you regarding the other support. Other than you should consult an expert.