Aaden: Of course it still is native if you match the horizontal resolutions and keep the image unstretched.
Oh, sorry, I didn't know you couldn't choose from any resolution in the Options menu.
I'm almost sure you tried that already, but you never know: Is there an entry in the user.ini like fullscreen=0/1? Setting it to 1, your resolution to 1280x720 and not entering the options menu afterwards(! because it will overwrite your user.ini settings) might work.
Unfortunately, I'm not at home, don't have TW2 here and can't look at the user.ini myself - so, I'm basically guessing from what I'd expect to be in the file.
You sure it's native? A monitor only has 1 native resolution. In my case it's 1280x1024. Anything other than that is not native.