Sorry, I didn't respond right away because this took a couple weeks after we got back to fully resolve. By then I was swamped with work and the holidays. My first time back to the boards today.
So onboard we went several rounds with guest services. All they would ever say is that they sent it to corporate to resolve, and they didn't give us updates when promised. We also tried the Yacht Club Director and he basically treated us like we were trying to scam him and that he'd never had to give an upgrade to someone in this situation, although he let slip that it was known that MSC has a problem with their upgrade process and that this seems to happen regularly, and there's no way to quickly resolve it for those impacted even though it's been going on for months. There were at least 3 others in line at guest services with similar upgrade issues when we were first in line at boarding.
The Yacht Club did send us a bottle of Champagne with an apology note several hours later, although we were still stuck in our original room at that point.
Halfway through the cruise corporate finally confirmed we were supposed to be in the Yacht Club. At first they tried to put us into a lower level suite than what we bid on. It was disappointing compared to the aft suite (non-Yacht Club) that we already had. We told them it was the wrong suite and we didn't want it since it still wasn't what we upgraded to. An hour later they offered us the correct suite and we accepted. So we got to enjoy both an aft aurea suite and a Yacht Club Suite in a single cruise. (And we loved Ocean Cay and Ocean House for lunch.)
However, that still left the issue of what we paid for vs what we got. We were assured later that we would get a prorated refund for 3 of the 8 days upgrade fee. However, it took until two weeks after we got back home from the cruise to get the refund. They did end up refunded more than they originally indicated to help make up for all the trouble.
I think what helped vs others in similar situation who never got their upgrade was we brought copies of the credit card statement showing the billing and the corresponding upgrade email with us, and they faxed those to corporate.
I would say that the aft aurea suite is definitely a nicer room than the Deluxe or Grand Deluxe in the Yacht Club. So doing it again would depend on what is more important, the room or the Yacht Club experience.
Getting off the cruise we were disappointed with the way MSC handled this overall, but since they did make it right in the end, we have decided to book with them again.