I completed the achievement a couple of hours ago (i collected 12 of the 13 skulls in Halo CE today, and the foreign skull probably a couple of months ago) and got all 13 specific achievements for each skull.
Still it shows only a 12/13 completion. I also played a few missions after collecting the last skull and also waited a few hours and even restarted the game but the achievement still won't unlock.
I had a similar problem few years ago.
The problem occurred after I downloaded my profil to my brothers xbox and back to my own again.
I then tried to unlock the Terminal and Skull achievements but they simply did not pop up.
I contacted Microsoft and they told me they couldn't do anything about it. I would have to try to inform the developer of the game. ... didn't work either.So what I did was I deleted the game and it's savings from my Xbox and I also deleted my profile from it. (Be sure your profile is saved somewhere in the cloud before you do that).Then I installed the game again and downloaded my profile from the cloud back to the Xbox.
So and that actually worked out for me. But not all the way through!
I picked up skull after skull and found terminal after terminal but due to "life" I could't play the game through in one piece which is why I had to turn off my console and continue some other time. At that time I was already half way through, meaning I played until the level 343 Guilty Spark.
Well, later I did continue but I discovered that the game is doing that same crap again and it did not unlock the achievements for finding all skulls and all terminals at the end of the game.
That is when I repeated what I did before (see above) and I had to repeat all levels again hoping it will unlock everything this time. Luckily it did.
So if this works out for you then just try to play through the game in one piece.