Pulling up on the pedals (pedaling in a circle) works hamstrings (back of upper leg.) The standing calf press that you're referring to works calves because the concentric action (pushing) in pushing the weight up. When you lower it, you are using eccentric action (fighting the weight from going down too quickly) which is very different from pulling.

Your calves may be more defined because you've lost the body fat covering them from riding - not from pulling up on the pedals.