I finished the scenario but the achievement remains locked along with other achievements I also earned during the playthrough like City of Man and Worse than London. Anyone else run into this problem?

Problem partially solved. I reloaded the autosave just before the scenario finished and I got most of the achievements I expected at the end except for City of Man which the game still refuses to grant despite me having 681 people at the end.

Got the City of Man achievement on my third playthrough of the A New Home scenario. Could the problem be the Refugee scenario?

Another unawarded but earned achievement in the Refugee scenario: Bread and Games. Reloaded and finished the scenario twice but still unawarded.

Counted at least 4 such achievements and I've already unlocked 48%. Played at least 10 times each scenario. Seems like the game is disconnecting from GOG Galaxy. It's not like you don't earn some achievements, it is related to the game - either you get all earned achievements at the end or you don't at all.

Probable solution would be to save before scenario end and restart Galaxy+reload the game if you didn't get any achievements. It would be also worth checking if Galaxy overlay works during the game. I'll test it and post my findings.

Did you end up trying this?

I was having some issues so reinstalled the game - played the Arks scenario from scratch and successfully finished it BUT the achievements such as Conservationist and Technocrat remained locked. Hopefully the GoG version will get the update soon (Steam ver already has it) and this will be fixed.

Sometimes the game looses connection to Galaxy. For example when I use MSI Aftermath+Riva Tuner, Galaxy overlay stops working. But sometimes that's not the case.
I've completed 73% [36/49] of achievements (you can check my profile, it's public) and some just simply don't work - you've got to do something else then description says. I've recently finished Arks on Hard, yet no achievement (Iron Man) has been registered. I've got a savegame just before the end, but reloading did not fix the issue. I've done plenty more, that were not awarded.