Achievement bugs

[Captain Lag]

I've just done a second playthrough of CE with a guide, getting every terminal and skull...
I just got the achievement for finding all CE skulls, and I had gotten the achievement for finding all terminals, but I didn't get the achievements for terminals 6 or 7, or skulls Recession, Black Eye, Eye Patch. I've done it in one continuation, normal difficulty, same skulls on each and every one, no 0x scoring skulls enabled. I'm very confused as to how I even have Headhunter and Dear Diary with those having not actually popped.