Zsrai: I've done that change on my desktop shortcut and it's stayed unchecked, maybe try that instead of the actual exe file?
H3RB3RTW3ST: I've done that. It checks itself back. That's why I'm so puzzled. I have admin privileges too. I'm just baffled.
This comes a tad late almost 2 1/2 years later, but I was having the same issue and after a great deal of searching discovered the problem.
There's a registry entry that's responsible for this.
(As always, beware editing the registry, you can destroy Windows, etc.)
HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows NT\CurrentVersion\AppCompatFlags\Layers\C:\(Install Directory)\(Game Directory)\KODP.exe
By default it's set to "640X480 DISABLETHEMES DISABLECICERO DISABLEDWM HIGHDPIAWARE RUNASADMIN"
I deleted everything except "RUNASADMIN." After this, I was able to make changes to the Compatibility section and make them stick.
Combined with jerfa's post in
this thread I'm now able to play the game, windowed, without having to manually change the screen resolution afterward.