Hey Sean, no has nothing to do with the mouse, I have two identical Logi Trackballs, one is used with this software one is used on a work computer. I can swap them same result. It is only noticeable on the machine that it is not connected to, on the primary where it is physically connected the scroll works fine, but when I go to a KVM machine that is where the scroll has issues.
Multiplicity just sends the wheel message from one computer to another so it should actually the same on both.
I would suspect if the Logitech software was not running on the primary that it works as expected as sometimes these additional helper apps detect the foreground app and send arrow keys instead or multiple messages.
Also check the OS settings for wheels in case the Logitech ignores this but input from MP is respecting it.
I do not recall hearing reports of this before, though trackballs are not overly common.