The variables thing was a guess of mine. Cause I noticed 3 things that led me to believe that.
1. The girl in the bathroom on a clean save the first time you go through her choices all is fine but a second time it doesn't matter what you chose the event continues as if you refused.
2. Noticed I seemed to miss some things in the gallery so I went back into the game couldn't seem to find it (I assume that is now fixed) and thus noticed :
3. at the end of te Seraphine scene when you go through it for the second time you suddenly miss the part of the story how much I couldn't say but I noticed I unlocked wonders when I went through it the first time and thus assumed something wrong with the variables being set there.
As point 1 and 3 remained consistent even after starting a new game or with different choices and only went away when I removed my save file, and so I reached a possible answer.
I will check the game out again somewere in the weekend and will let you know ifI encounter something strange.
Good night.