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Running Win10 64-bit, with GTX970 updated to latest drivers. Got a similar problem here. No CTD, but defaults to 800x600 whenever I run 1920x1080 in full screen.

Running windowed, switch to 1920x1080, restart then set to full screen doesn't work. Resets to 800x600 immediately.

Manually changing to .ini to 1920 x 1080 also didn't work, it simply runs at 800x600.

This is forcing me to use a lower resolution (I settled for 1764 x 992, not sure why this presented itself as an option). Works OK, but still bugs me why I can't run at 1920x1080.
I'm Running Win 10 latest build Resetting to fullscreen and 1080p. the exiting game and the setting to fullscreen worked for me. as stated above. after running a bunch of changes I repared & verified files first through GOG galaxy!