Also, make sure you're running the right executable. I made that mistake once, running the vanilla Sins client, and I wondered why the ship-building icons were in the wrong places... it took me a minute to realize I hadn't started Entrenchment. (They re-odered the icons to Capital/Frigate/Cruiser for starbase reasons.)
The one you want is "Sins of a Solar Empire Entrenchment.exe", with a different icon than the original one.