For the Vaulters every time I get the Discovery Mission quest for the faction line of quests after searching the specified ruins the armies that 'wont leave me alone' never spawn therefor the faction quest line cant advance. Whereas when I get the quest to build two strategic extractors the enemies always spawn and the faction line of quests can advance. I have reinstalled the game twice now but the bug persists.

Save game ?

As the nice man said, please upload your saved game zip file so we can look into your issue. :)