Basically, all the versions of glest have a value in the ini for screen resolution. I strongly recommend using the INI for all settings, since it is vastly superior to options menus.
By the way, it is worth mentioning that the resolution needs to be in the same aspect ration as 1024x768 (4:3). If you try and use a 16:9 ratio, it STRETCHES all the images (but not the models, display, etc). Fortunate for you, 1600x1200 is a 4:3 ratio.