Forum:Hidden Valley glitch??

I have just completed the first part of 'still in the dark' and have betrayed McNamara to Hardin, and have asked to join the brotherhood. however whenever I leave the bunker and return, I find that the self destruct has been activated while I was away and none of the indicators for this (for instance a large explosion or all my quests failing) have been activated. What's going on? Has this happened before??