Okay, so I've seemed to of fixed the problem. I deactivated 'Duel - Combat Realism 5' 'Revamped Vampire Lord' and 'Reduced Distance NPC Greetings'. I then loaded up my Autosave from entering the Castle and did the tutorial again, this time doing nothing at all except what was asked of me on screen, did not even look at the cattle. Now everyone seems to be happy with me. I saved and reloaded right in the middle of the dining hall with those three mods reactivated and everything is still okay. I think that so long as you pass the alliance check or whatever it might be in the background, and are confirmed as a Vampire, mods should be able to work again.
Hope that helps anyone else who has this problem.

If it doesn't work, try this; http://forums.nexusmods.com/index.php?/topic/751549-dg-vampires-attack-me-after-joining-them/page__p__6001769#entry6001769