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.

I have experienced this issue on my second play through on the PC version of the game. The problem seems to have something to do with wearing power armor and a companion in those cut scenes (which is weird because I was wearing power armor and a companion in the first go around). In the quest to confront Kellogg, combat would start immediately when I entered his room. The resolution to the issue was several things. I backed up to a save before he opened the final door. I made sure that the my companion was several rooms away and on Stay. Then I jumped out of my power armor and destroyed the ceiling turrets. This time when I entered the room, the dialog processed correctly. It took several tries to get it to work correctly.

I am wondering if I had some perk on my second play through that caused this problem. I have had the issues with other scenes where an NPC starts dialoging and then enters combat randomly. I think it may have to to do with intimidation perk which gives you the pacify option on a weapon. I don't know. I hope this helps you get to the dialog.

Ill try exiting my power armor and see if that does anything for me. Thanks for the reply!