I have completed the single player game on all difficulty settings, I believe I was running version 1.03 when I beat it. All races were unlocked.
With version 1.04 the Alliance and Empire races are no longer available to me. I was the Alliance before the patch, and still have that selected as my race, but the option to choose them is grayed out. I can load alliance ship designs previously built, and save ship designs to a new file. I can not select hulls from the Alliance or Empire.