Whilst it doesn't help the OP, I don't think that this is particularly an integration issue - more a dodgy computer system issue.

Last October my wife and I were traveling IAH-LHR and had both requested mileage upgrades from our B fare. Upgrades didn't clear in advance. I checked in on-line and was immediately added to the waitlist. Checked my wife in and she didn't get added.

Several phone calls later I was assured that although we can't see her on the list, she is on the list that they can see. Hmm.

Arrived at IAH as boarding was just commencing. I was handed my new BP but was told my wife hadn't cleared. Last time I checked I was #1, wife should have been #2.

I wasn't a happy bunny and the GA passed to to a more senior colleague. I explained that she should have been #2 on the list but other people were getting upgraded. Eventually he said "The system isn't recognising your wife's status (She's Plat)". Luckily the flight wasn't full and he processed an upgrade for her.