Yeah, I'm getting the same problem... 
I'm going to fire off an email, hopefully this isn't as bad as when lucas arts managed to screw up 5 different keys, and then made a total recall... 
Edit: Ah, okay. I've managed to fix it, basically once you get that error exit the setup file and go to the support website for stardock. https://www.stardock.com/support/index.aspx - From there retrieve your serial numbers by entering the email address that you registered with. Go to your email and then just above where your serial number is is a link to a download file for the impulse setup. Install Impulse and then go into my games and Sins of a Solar Empire will be waiting for you.
I'm not quite sure why this bug wasn't found before production but it only takes two minutes to solve.
I hope that this helps - Andrew