I now own the X1900 XTX card and I discovered one quite important thing considering 3D. The card uses clock of 500/600 when in 2D mode and clock of 650/775 when in 3D. Although, 3D FULL SCREEN. And not windowed. So basically, if you flying in windowed mode, you are not using full potential of your X1900 card.

I have a 1800xt and its the same with clockspeeds being lower in 2D mode, but the performance is exactly the same when running FS9 in windowed mode or full screen.