I did the quest 'Still in the Dark' by walking into the bunker, meeting McNamara, and chasing the ranger away. Then I got the holodisks from the lost patrols, showed them to Hardin, and told him about the Chain that Binds. Hardin tells me to come back in a few days, and when I do, they immediately open fire on me. I'm not wearing any faction armor, and I have a positive reputation with them. If I walk in naked and companion-less, they shoot at me. If I go into the bunker with Veronica, they shoot at me. Even after using the console to set my BoS rep to +99999, they shoot at me.