Yes, there is a difference, but...
I've been running an IOGEAR MiniView SE KVM for years - cost me, like, 200 bones. Still works great! They'll have to pry it out of my cold, dead hands - I digress...
Anyway, I have a dual output video card - half VGA analog - half DVI digital. Dittos for my Dell monitor - dual inputs - VGA & DVI.
So, I hook them both up - VGA through the KVM, and DVI directly to the vid card. That way, I can switch inputs using the monitor control buttons whenever I want to run one or the other. Make sense?
You didn't ask, but I also hook my lappy up to the KVM using a USB-PS/2 adapter and VGA. Works great! I can use my desktop 'K' 'V' & 'M' on my Toshiba Notebook, instead of wearing them out...
Simple pimple...