For those in the Beta:
https://forums.flightsimulator.com/t/1-37-8-0-regression-fixed-in-1-37-9-0-custom-window-size-being-reset-every-time-app-is-started-also-fullscreen-mode-reverting-to-windowed-mode/633921
Issue is fixed.
Non-Beta:
https://forums.flightsimulator.com/t/sim-always-defaults-to-windowed/634730
Issue will be fixed in SU15