You are absolutely correct unless SPG has had a major change in the rules. You are actually entitled to points for up to 3 rooms if you are paying all the charges. Night and stay credit are only for the one room however. You could talk to the Hotel Manager before you leave or just make sure you get the closing statements for both rooms when you check out and contact Customer Service when you return home.
The St. Regis Grand is a wonderful hotel. Hope you have had a great stay besides this misunderstanding on points.