How can two machines appear identical and yet not have the same actual mechanical advantage

There are many factors which contributes as to how a machine will be processing the input energy and convert it to output energy. Even with identical mechanism, these factors will have major effect on the output. Some factors are deflection, friction and wear. Some system maybe exposed to poor lubrication than the other which'll produce more friction and wear thus lower mechanical advantage.

Kinetic energy = 1/2mv^2. since the mass is constant we can form a ratio of it's kinetic energy at 60 divided by that at 30 to see ke(60)/ke(30) = +(60^2)/30^2). this may be said to 300% increase.