moving coil or moving magnetic input.

Are there any differences in terms of sound quality if you are using a moving coil cartridge such as the Benz Micro Ace(Medium output) and plug the connectors into the MM inputs? The reason I ask is that the moving coil input's on my preamp are malfunctioning. I plugged into the MM input and other than a slight gain difference it appears to sound fine. Is the gain issue the main reason to use the MC input section?

Cheers,
Nocaster