After I defeat the Behemoth, the BoS stay allies for a short bit, it seems once Sentinal Lyons speaks to Paladin Vargas about Initiate Reddin's death that the BoS becomes hostile. I've checked things such as, not blowing up any cars, picking up Fatman and NOT using it, but neither seem to affect the eventual outcome. Also, Knight Captain Colvin dies. I thought he's supposed to be essential at least during the GNR battle.
Here is my load order attached. CCO stands for Cirosan's Classic Overhaul and IWS stands for Increased Wasteland Spawns. If anyone can help and/or has experienced this problem, let me know. As it stands, I can't really do the main quest in DC.