JunePaik: On Steam there was a patch 1.13 released on September 25 and it's saying this in patchnotes:
"Fixed various progress-based achievements which appeared to reset when the game was closed."
So they definitely do bother fixing bugs.
Anyways, it seems this patch is not released here on GOG yet since we still have the bug. So I'm wondering when they gonna do that. Actually I'm not sure what's the current game version on GOG. In the Galaxy it's just saying Update 1.
When I talk with support about this issue, they promise to investigate. So I hope we'll see this patch on GOG too.
Btw, they, I mean support, asked me which achievments is supposed to be unlocked and unlock them for me. I believe, you can ask them for the same and remind them about this patch ;-)