I do not follow you example, but you have some ini settings to force the game to run at desktop or to set the resolution.
KeepRes=1
Can be 0 or 1. If 1, your screen resolution is used for the game instead of the default 1024x768.
VideoMode=1280
Can be 1024, 1152, 1280, 1600, 1792. Changes the game's resolution to the value specified (instead of the default 1024x768).
Refresh=70
Changes the default refresh rate of your monitor. Do not change/add this line unless you are experiencing problems!