Hi @Deadmanstroll ,
Right, that cleared those screenshots up for me, thank you.
Still, I don’t know exactly what’s going on. Booleans are very finnicky, but a difference between Solid and Wireframe is weird. Maybe a Face that is Hidden (in Edit Mode), that is covering the holes? Far-fetched, I know.
If you could upload your .blend (Dropbox, Googledrive, or so) and post a link here, we can have a look.