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I have spent hours adjusting settings, so now I'm at the point where the game (madden 08) looks great in a smaller window, but once I make it fullscreen it appears to go back to native resolution. Does anyone know a method to fix this?

If you haven't already, go into graphical plugin settings and set the native resolution to 3x. Worked wonders for me. Setting anisotropic filtering to 2x and enabling anti aliasing in nVidia settings have worked wonders for me.