This is on Mac (o specific tag available)
When, during a game, you look at a different deck, it will be preselected once you start a new run. If you had a higher stake on the previous game then is available for the new deck, the little dot below the stakes will be gone, its back when you select a stake, so its really no biggie.
Edit: When you decrease the stake from the invisible one, it won't jump to your highest available stake, but each click will decrease by one unavailable stake, you only get the dot after jumping through all the unavailable ones.