I was staying for six nights at a St Regis when the system changed over. Despite being told it wouldn't be an issue - no surprise no points were awarded for my room charges as they were charged at check in under the old system and half of my night credits are also missing. No one knows how to solve this.
I have a LC stay later in the week which was a prepaid rate - I have subsequently been charged again with the system change. I'm confident about this one because I can easily raise this at check in and won't have to deal with Marriott.
To complete the trifecta I have five nights at a LC checking out on 1 Jan - I have applied my final batch of SNA expiring 31 Dec to this booking. I now have two seperate bookings showing one with the SNA pending and one without - I'm sure this will work itself out