The Patch Project 1.2.6 is going to feature widescreen resolutions. The current version 1.2.5 does not.
how do you know it is not 1600x1200 when you apply the resolution? some tfts show the current resolution in their OSD, you could take a look there.
i assume your question is the same over at fleetops.net
Star Trek Armada II: Fleet Operations - resolution