Thank you for your replies. It does seem to have something to do with the story heights, because as long as I place the modules in plan while on 0. story, they keep on behaving properly even in 3D, they can be moved up and down without any trouble. I have noticed though when I happened to place a module in plan view story 1, the "compressed" floor occured. This must be because the stories of the module are not identically high, the middle story is 25 cm lower.
As for the window behaviour, it remains a mystery. I´ve checked the anchoring and it was from wall base, I´ve never used any other option. Now the problem hasn´t occured for a while. But before, I even had ghost extra windows in the air outside the module...
So the conclusion is that you must be careful with story heights. Am I actually not supposed to move the modules up and down once I have placed them?