Yes, you should be getting your points for both rooms (assuming the rates are point earning rates of course.) Marriott T&Cs state that you should be able to receive points for up to 3 rooms per night. With that said, you might not always get night credit for both rooms. The T&Cs state that you should only get night credit for one room per night, but quite often Marriott's system will give night credits for both rooms when they are at different hotels (though recent posts in this forum seem to be showing that Marriott is starting to catch those mistakes more than they used to.)

Give Marriott Rewards a call. Their system should be able to find your stays and make sure you get the points you should have received.