I am in the exact same situation as you.
I have pre-ordered Sins of a Solar Empire Rebellion on 07/04/12 from steam. Downloaded, installed the beta game through steam and created a Stardock account on the stardock.com website.
When I click to play the game a minimized window comes up titled Stardock Account Registration, enter my stardock account email and password then click register. Sometimes the window disappears before I can enter my details but when I enter them quick enough by pasting in my email first then typing my password in very quickly it shows this message "sins of a solar empire rebellion registration was successful"
So when I click to play the game again it shows the same minimized window titled Stardock Account Registration asking me to put in my details to register again when I already have ?
I submitted a ticket to firstname.lastname@example.org and someone dealing with my problem with no success yet.
If you do manage to solve your problem please message me back.