I can understand how some of the OPs issues may have occurred. Reserving 2 rooms with one paid and one award, the hotel may have "assigned" the OP to the award room thus no night/stay credit. But they could still get points for the other room. Not saying that is right, but it was a little out of the ordinary.

In my experience hotels seem to like to mess up points for package rates that include items they won't give points for.