I got as far as the end of the first quest for them, after finding the parts from the various vaults and retrieving the scouts stuff the elder was convinced to start investigating the surface, he asked for a few days.
I went to the head paladin fella and he said he'd use the stuff I found out to overthrow the current elder, asking for a few days.


After about two in game weeks I remembered the BoS and went back to see how things were, there was a patrol of 4 paladins on the surface but when I went to the elder it was still the original. Neither him nor the head paladin would talk to me, their out of conversation dialogue asking for a little time.

I waited three in game days at Novac then went back, no change, have I missed something or is it just another bug?

Did the quest say it was completed when you brought the parts back and talked to the original elder? If it did then that's why I think your getting this issue. I think you need to talk to hardin before completing the quest since his part is the (optional) part of the quest. If you read my post that I just made "Quests completed, but not...." I have a similar issue except that I successfully helped hardin overthrow, but that other dude keeps asking me if I have found the parts for the ventilation system. I think the problem is that they didn't properly script the game to te up the loose ends if you did optional parts of quests etc.