For me the difference was not in the shoe but in the pedal. The MTB pedals I was using (Shimano SPD's) did not offer a wide, stable platform and that allowed my foot to rock a little from side to side. After an hour or so of riding my right knee would start hurting. I switched to Look road pedals and the pain went away. I can ride for hours now, no problem. On the MTB I've never experienced that issue, probably because I don't usually pedal the MTB for more than an hour straight - there are always places where you have to coast or sometimes even get off and port the bike so it doesn't come up. I've also found that while both the SPD's and the Time MTB pedals I use now have float, they also have notchy feel that tries to force my feet to a certain angle. My Looks don't have that issue - they free floating up to 9 degrees.