Originally Posted by
stifle
The earning style you have on file (points and miles or points and points) at checkout determines whether you get points and miles or points and points.
The airline partner that gets stored with your booking is the preferred airline partner in your profile when you book, but only if you have points and miles selected when you book. Otherwise, nothing will be stored.
The airline partner that gets credited with miles (if you've chosen points and miles) is the airline partner stored in your booking. This will be the same as the airline partner in your profile if you haven't changed the profile or the booking between booking and staying. If you have, it won't. I absolutely guarantee you that if you have BA as your preferred airline partner in your profile and give a VS number at check-in, your points will go to VS. I have done precisely this when I needed a few extra VS miles once.
Only if you have no airline partner stored in your booking (for example, because you has points and points selected when you booked) will it pull from your profile. This has also happened to me when a travel agent booking did not include my HHonors number. I gave it on check in, and it pulled my preferred FF number from my profile.
In my previous example, I had BD as preferred partner when I booked, and VS as preferred partner when I checked out. I said nothing to the desk, and the miles went to BD.
If you believe you have a contrary experience, then the most likely interpretation is that HHonors IT is bugged
Yep, this is correct (and I've confirmed this with the Diamond Desk). The
earning style is connected to your profile at 11:59:59pm Central Time on the day of your check-out. The preferred partner is connected to the individual reservation. I booked a stay last fall for this past March and had WN as my preferred partner when I made the reservation. Of course, that partnership ended as of Jan 1, so my new preferred partner automatically changed to Delta in my profile. This did not update in the reservation, so even though I had Points + Fixed Miles selected as my earning style, I only earned 10 points (since the reservation had no preferred airline partner).