Ok I am going to have to use some spoilers to paint a proper picture of what is going on here. Any scene that staves off combat for a dialogue scene (such as stepping out of the vault after rescuing nick, meeting the old BOS paladin in the bunker, confronting Kellogg or when you go into the iron slagworks for the first time) the dialogue will not trigger, instead I am immediately attacked and combat starts. This is without any mods, I wouldn't even know that something was wrong if it were not for the fact that I have finished the game on the console version so I know that the scenes are supposed to be there. So far it has only caused a minor annoyance but it would be nice to get it fixed if possible.