I had the same problem, and I couldn't get SDC to show me the non-beta version, even after unchecking the "show pre-release versions" checkbox. What I did was download the 1.0X.010 patch from the downloads link above (it's erroneously called Collector's Edition Bonus Pack for some reason), and install that. That didn't fully work though, but now in SDC it had my version as 1.0X.010. Then I right-clicked on GalCiv II and clicked "Download and archive", which got all the files for the 1.0X.010 version down again, and archived them. Then I did "restore archive", and it fixed it!
If, unlike me, you happen to have been clever enough to archive previous versions before, you won't have to go through the downloading step.