That was kind of odd. I loaded it up and the homeworld space dock and starship constructor showed "Pause All" next to them and, indeed, didn't build anything. But the CTRLS screen did not have the pause-all-constructors box checked. I checked it, saved controls, and it stayed paused. I unchecked it, saved controls, and it unpaused them and they resumed building. Does that work for you?
I don't know how it got stuck into that mode.