I dunno if we should go the route that unauthorized persons are simply not allowed to know - seems kinda unnecessarily harsh. Still, I do think that having some in-story means of explaining the discrepancy (as Area82 was suggesting) isn't a bad idea; having it be a side-effect of the time-stop seems like a pretty decent approach.
As for Weirdo's suggestion, I don't want things to get too unnecessarily Wagnerian epic-scale, but having Hawkins (or probably rather Cecilia, who would be an obvious spotter for a discussion like that in the AI community) clued in would be a decent story bridge to bring the two halves of the Numbers together, if we're ready to move that plot toward its final stages...