Let's use logic to figure this out.
There are two types of Vibranuium, both extremely rare.
Vibranium was first deposited on Earth by a meteorite 10,000 years ago. The first documented discovery of Vibranium was during a human expedition to Antarctica
. This particular isotope of Vibranium was dubbed "Anti-Metal" due to its property of dissolving other metals.
A different variety of Vibranium is found in Wakanda.
Howard Stark told Captain America how rare Vibranium is, and Howard used all the Vibranium he had to create Captain America's Shield.
Remember when Tony was watching the film of his Father?
Howard Stark said, " it represents my life's work. This is the key to the future. I'm limited by the technology of my time, but one day you'll figure this out. And when you do, you will change the world."
I believe that Howard Stark figured out a way to manufacture manmade Vibranium, but did not have the tech to make it happen in his time.
My answer is, Tony, with modern tech, was able to create manmade Vibranium and used that to replace palladium in the arc reactor.