This is still a problem today, five years later, in 2020. I had to hunt for the correct config.cfg file — I found several, and had to delete them all simultaneously. Apparently my Documents folder is in the OneDrive Cloud and the GOG Cloud and one or both of those services kept rewriting and replacing the deleted file with the broken version. Here’s where I found mine:
C:\Users\alex\Documents\Battle Brothers
C:\Users\alex\OneDrive\Documents\Battle Brothers
I note also that these are different locations on my disk and some games files (log.html and version.cfg) seem to be written in one and others (savegames) seem to be written in the other — or both? This is buggy code and I wish you’d either fix it, or open-source it so the community can fix it ourselves.
Update: to unify the directories, I had to delete one, and link the other, like this (from console as administrator):
cd C:\Users\alex\Documents
mklink /J "Battle Brothers" "C:\Users\alex\OneDrive\Documents\Battle Brothers"
Junction created for Battle Brothers <<===>> C:\Users\alex\OneDrive\Documents\Battle Brothers
