I suffer the same when I'm running any mods. I personally think it'd due to reloading all the information again, but don't quote me on that.
Anyways, you're here for a solution. I've got two for you:
#1 - run vCoH and change the setting there
#2 - open "configuration.lua" in "Documents/My Games/Company of Heroes Relaunch" with a text editor, and change the settings there manually (some of the settings are a bit decieving - so make sure you're changing it properly).