"Your United Mileage PlusŪ Account XXXX was used in this reservation."

My belief is that those three specific hotels I'm staying at in San Diego are using a different reservation system than some others in the chain. I also am in the belief that regardless of my affinity program, Choice is communicating my Choice Privileges # to the hotel, which is getting picked up by their reservation system rather than my airline miles.

Alternatively, I've been staying in lots of other choice hotels -- and only those three are having the problem with posting to my Choice account rather than my airline mile account (And all 3 are owned by the same company) -- I think its safe to say that you should ask at checkin/check out just to make sure your proper affinity affiliation is in the reservation.