Here, I zipped up
two config files. One is the stock DoomConfig, since this one should stay untouched. The other is an autoexec.cfg that sets the resolution and nothing more. Unzip them to your ".Doom 3base" directory and see if it works. You can add "+exec autoexec.cfg" to the command line if it's not loading automatically. Bring down the console once you're in game and enter r_customHeight, r_customWidth, r_mode, and r_aspectRatio to make sure they have been set correctly. You can also Pg. Up in the console to see if your config file has been executed when the game has been launched. Keep in mind that the options will show your resolution as 640x480 when r_mode is set to -1.