My monitor is 5120x1440. On first startup my resolution settings were correct with no fiddling necessary. While in fullscreen mode, I once switched the resolution to 1920x720 to play on another screen. From that point on, my resolution in-game would show as 5120x1440, but it would actually be displaying a 1920x720 image stretched. While in this state, changing the display resolution setting would prompt allowing me to "apply" a new resolution, and the game would ask me if I would like to revert to the previous resolution, but no actual change would be made to the output image.
Switching to borderless fullscreen mode and back again got me out of this glitched state and allowed me to actually change the resolution again.
I was able to resolve my issue by changing the resolution under fullscreen mode once out of the glitched state. Now my game starts in the correct resolution, but the glitch is able to be consistently reproduced by changing the resolution to anything non-native while in fullscreen mode and then exiting the game.
Bumping for a fix! I believe my issue is related to your issue, though I know yours is with borderless fullscreen mode. Hoping this helps you in the meantime.
