You probably have a different video driver since you originally installed Sins. If the driver doesn't return it in the query it won't show up as a choice but you can force it by shutting down sins and opening up user.setting with notepad and hand editting the resolution fields. User.setting is likely located here:

C:\Documents and Settings\username\Local Settings\Application Data\Ironclad Games\Sins of a Solar Empire\Setting

or

C:\Users\username\AppData\Local\Ironclad Games\Sins of a Solar Empire\Setting