There was only one time I booked more than two rooms at once. I was handling the arrangements for a small group. I booked different combos of rooms on several different reservations, like you did, but then immediately followed up with a phone call to the hotel's sales department. This was to (1) avoid the misunderstanding that apparently bit you, and (2) to see if they could do better on the rate. I was successful on #1 but not #2.

When you arrive, try to get the front desk to put all the rooms on one folio, so you get the points for all of them.