Are all you bikes flatbar? Any dropbar bikes in your collection? Reason I ask is...decision as to what bike to buy in large part hinges on geometry. In the case of a drop bar bike...that means saddle to handlebar drop. Amount of drop affects head tube length...very important. Generally the amount of drop you can tolerate is a function of flexibility more than strength.
Do you run drop on your flatbar bikes?...if so how much?
Also...since you have your knee issue on two different bikes...one also with a lot of gears...you maybe pushing too much gear. It could also be your position on either/both bikes and also cleat alignment. Knees are fussy about proper mechanics and technique.