The Archivists didn't call the FBI first? It makes me wonder why. Are the keepers of our highest Archives in cohoots with the x42 administration? It sounds like one whole shift was part and parcel of this theft. The second shift seems to be the ones who caught it. It this right?
That allegation you suggest has been made, although I am not sure if we know the actual logistics of Berger's heist, as yet.
I'm inclined to believe they just couldn't believe it (if they were Freepers they would have right off the bat!), but they were concerned enough to do the markings and watch him carefully. Perhaps they felt they needed to have evidence before going to the authorities for fear they wouldn't be believed. The fact they did set him up makes me think they were not in cahoots.