This sounds very similar to what I just encountered this weekend.
KVM to switch between A&B, but also using a Radial SW8-USB to auto-fail. Very time I switch screens, it also fails over.
Tracked it back to what appears to be an issue with the KVM not presenting a stable EDID to the computers, so they see the display "change". In my case, it is advertising (or stops advertising) HDMI audio out. Even though I am not using it, every time it happens Qlab adds/removes HDMI (and adds back all the other audio source I am not using) from the audio list and the audio glitches.
While the screen resize can't be helped - that is an OS function, and probably part of your issue - I am running in show mode with "Disable disruptive OS functions" Enabled (4.6.9) and this is still causing a reconfigure, even though I would expect it to be ignore based on the preferences.
Jay