My understanding was that her powers worked in a quantum fashion where she was able to chose(perhaps passively without thinking about it) what reality she was in amongst all possible probabilities to suit her goals.

This is not how her power works. Contessa is a precog. Specifically, the way the PtV shard works is as follows: Contessa asks it a question: "Path to making the perfect grilled cheese sandwich" for a (silly) example. The shard then looks into all possible futures and picks the one that best suits the path chosen. It tells her what steps are required, guides her in making them, and lets her know how many there are.

If the Path Contessa makes isn't possible, her power returns a null. It doesn't function properly when used on Entities, Endbringers, Eidolon, or people whose powers block precognition in specific or Thinker powers in general.

We can readily assume that it is in fact possible for Yugi to lose, so the first failure condition isn't an issue. Yugi isn't an Entity, an Endbringer, or Eidolon, so the second failure condition isn't an issue. The only problem left is the final failure condition. I'm not really familiar with Yugioh so I can't directly say one way or the other if Yugi's particular brand of bullshit will trump Contessa's own brand, but I doubt it.

If she shuffles her own deck, whatever cards she needs to win on the first turn will be on the top. If she shuffles Yugi's deck, it will be in the exactly worst order for Yugi. If both decks are randomized by a machine that she has no way of interacting with, she will make whatever the optimal move is.

If Contessa's power isn't blocked, she wins 10/10. If it is blocked, she loses 10/10.