It was the newest Patch of the Game.

I started downloading the Patch but did interrupt it and play the Game, i've got to an Secret and saved right before i found it.
I had no Archivement.

I quit the Game, let the Patch install and loaded that Section, i've got the Archivement.

So it was the Patch ;)

Gog itself was patched before.

This means you have to do them from Scratch, as it doesn't count for what you've done.
I personally don't care, but it is imo funny having a late Game Archivement without any other :)

It can be also viceversa.
I bought Ion Fury here on Gog and played through, later i bought the physical Version, that brought a Steam Key.
I just connected the installed Gog Folder to Steam, started the Game and i've gotten all the Archivements.
Beaten the Game in half an Hour, i am the new Speed Runner Kind haha.
Oh i had that Error, was really annoying to redo all the Launch Options for Doom and some others.
But well, Sheets Happen, overall i am pretty content with Gog Galaxy and this Feature.

Glad that fixed the achievements, shame I'm quite far in the game and some will require to play game again.

Some achievements still seem bugged. I beat the game with difficulty set to 3 for every category, and didn't get "Don't Forget to Salt the Fries".

Which is brutal, because that one is tough.

You can always contact GoG support, once they check they will unlock it for you.

No achievements can be unlocked for me because the GOG Overlay never even loads in the first place. Has anyone experienced this issue? I made sure to update the game to the new patch and I reinstalled GOG Galaxy to the newest release.

There is no Overlay for System Showck Remake.
Achievements do work after latest patch.
Check your PC firewall settings.

The overlay is not needed to unlock achievements. As an example: The overlay does never work in Everspace 2, but the achievements unlock through GOG nontheless

Have you actually successfully done this with any game? And if so, recently?

I tried and just got the canned response "Unfortunately, the playtime and achievements cannot be edited manually and that required a lot of work from our developers, therefore we do not offer the option to edit time or reset achievements on request."

Just to see if it was a fluke, I even did a brand new run yesterday, beat it again on highest difficulty for every category, and it still didn't unlock.

Some others still seem broken as well. I've definitely hacked more than 20 targeted enemies, for example. But at least if they ever fix that one it won't take 10 hours.

"It's Over" also still seems to be broken.

Well, I can confirm that achievements now work. 21 hours in, and I got the achievement for solving the chess puzzle in Delta Grove.

Yes, I've opened support ticket about not working System Shock Remake achievements, and at least twice got offer to adding achievements manually, thats why I suggested this option ;)
Seems that every support person have their own response to support tickets.

Hacking enemiest achievemnts works, got it recently, most probably works same way as killing 10 enemiest with berserk buff. Can't be done with save / loading (most probably)

I suggest opening support ticket for those non working achievements.

Thanks for the tip, I wasn't sure if you meant never save/load in general, or like the same enemy doesn't count when you save/load.

Either way, I hacked 10 enemies without saving or loading period, and it unlocked.

glad to hear it got all sorted out. I took a break after beating it (and then the patch came out a few days later) and was planning to do it again to make my way up to 3/3/3/3 so hey, I guess I'll be able to get all the achievements just fine now!

at least it was something that was accomplished

There is another post about "salt the fries" and how to get that one, its actualy some kind of workaround but it works.

Thought I'd butt in to mention that I have had an experience contacting support about such an issue and they were very responsive, though also it was a nasty one. During the latest Christmas holiday season I was playing Cave Story+, and the achievements kept completely resetting whenever I started up the game. I suspect this was related to the game having an achievement for playing it around Christmas which was also triggered at startup. But yeah, I got prompt responses and the issue was fixed within a few days.