Do you have any of the output EQs set differently? Are your outputs all using the same source in the Kemper? Are you recording into the same input on your interface, same levels out from the Kemper, same level on the interface, etc?
I don't think I've ever touched an "output EQ", where do you find that? Does the Monitor Out have a different default EQ than the others? Other wise, yes they are set to Master - Mono (except for the Main Out which is master stereo but I use just the L output). Going into the same recording interface input, same everything. It's not a huge difference, but its noticeable, enough to make me prefer it.