I have the same problem: I bought all my games directly from Stardock (before the sale to GameStop) yet none of them show up on the new Stardock Central. This includes:
Sins of a Solar Empire (plus the two follow-ups)
Galactic Civilization II
Galactic Civilization II Dark Avatar
Swords of the Stars Complete
I have several other games from Stardock that are not currently installed, but none appear in any of the SDC windows even after refreshing. I found this odd because the old SDC had no problem identifying all my games.
Note: all of my games (and their serial numbers) appear in the Stardock website under "My Downloads".