AlchemistKitsune: Adding myself to the list. Got the popup at the end of the run, but no unlocked character. Using offline installer as well. This needs to be fixed. I do not use Galaxy, don't want part of the game locked behind some launcher wall if this is the case.
Wrote to RedNexusGames on Facebook about the problem, they fixed it (at least, for me) in the 0.9.13a version. They were very kind and the issue has been fixed in less than 24 hours. Hope it fixes the bug for you too guys.
Oh, and I had to unlock the new characters once more after the patch to get them, my first unlock didn't count.