(Disclaimer: The answer to Vulgate questions is often found in the original text. I know no Hebrew and will just attempt an answer from an inner Latin point of view.)
In historical narration, if an indicative follows after cum, the subordinate clause specifies the time of the events in the main clause, with there being no further relationship between the events in both clauses. A subjunctive on the other hand should follow when the events in the subordinate clause somehow affect or at least form the circumstances of the events in the main clause.
(Eo tempore) cum Columbus in Americam pervenit, Martinus Luther Latine discere coepit.
(At the time) when Columbus arrived in America, Martin Luther started learning Latin.
Obviously these events are completely unrelated, and the author does not wish to suggest otherwise. On the other hand:
Cum Columbus in Americam perveniret, Indiam invenisse putavit.
When Columbus arrived in America, he thought he had found India.
These events are related, therefore we use the subjunctive.
With that in mind, I think you will agree it would be surprising to find the indicative in your example from Genesis: The flood started because the announced period had elapsed. It did not coincidentally start when an unrelated seven-day-period happened to be over.