Just keep trying on the huge multi... on my first try at that scenario, there were 14 artifacts (obviously, 5 were duplicates).

<---- First time poster here.
I have gotten all of them in one game. I made my own map with 297 planets (-.-') to be "guaranteed" to get them all at a victory. However, now that I got all of them I still didn't get the achievement. why is that? I just wasted almost 13hrs to try to get this achievement and I still didn't get it. I had all of the 12 artifacts, I had doubles on three or four of them even.

The game was all ready won (obviously) since I had to colonize roughly 250~ planets to get all of the artifacts so I'm just going to assume that that's not the issue.

Do any of you guys have an idea? It is a VERY frustrating achievement to be stuck at. 

Actually I think it is the issue, but not the way you think it is. Achievements that are not won by doing X at the end of the game are actually given to you the moment you meet the criteria (AKA own 12 different artifacts), not on game completion. However, I think this only counts for games still going on. Once you get the victory screen I don't think the game still checks for achievements (since you're not really fighting with anyone anymore). Granted for this particular artifact, that makes no sense, but it is what it is.

There is certainly nothing wrong with using the GalaxyForge duplicate your favorite nonrandom map with 100% artifact density to get this achievement, especially after you've technically already done it. You can also just manually change the achievements file but that's no fun.

It is possible to get this larger achievement on the game's stock maps, but only on the largest map: the 132 planet Huge Multi-System Random map.  I know because I've done it at least twice now.  Once because I lost my old 100% achievement in one of the upgrades, and wanted to restore it. 

But I would recommend saving the game near the beginning, and counting to make sure there are at least 12 artifacts present, (by looking at the replay, etc.) and even then its not a guarantee they will all be different.

You don't play much Advent or Vasari do you?