Right, so achievements still not triggering, and I think it has to do with having two versions of the game on my PC at the same time.
When I push Ctrl to skip seen content is skips even though this is my first time playing the Steam version. Steam must think I have these achievements already or something. So, the question is, how to reset the Steam triggers for the cheevos.
*edit*
OK, even more strangeness to report. Started a new Steam game but tried different choices from those I made in the old version.
Still no achievement unlocks until the cafe scene with Nora, then like 8 popped at the same time, but they were the opposite of the choices I had made in that game so far. They seemed to be reading my choices from a different play. Also got the monk achievement, which is for rejecting everyone through the entire game. I noticed that like 70% of players have this, so that trigger is wrong.
After this scene it started to give achievements based off my actual choices, and it also stopped letting me Ctrl skip through content. So there is definitely some interference from having the old version of the game on my PC, unless it's something else making my cheevos go crazy.
Finally, I turned off Walkthrough in Steam version, but it was still showing up for some choices, which seemed a bit strange.