They couldn't have made a new queen and have her laying in 3 days.
I have seen bees clean the markings off a queen, but this obviously depends on the substance used to mark her.
The more likely scenario is that when your package was made, they shook a queen into it with the bees. The bees remain loyal to this queen and killed you new marked queen.
It is also not uncommon for queen producers not to use the standardized marking colors