For some reason, when I place a token on top of a card located in a deck, the card vanishes, but when I move the card outside the deck I can place a token on it no problem. The card has a layer = bottom and the token has a layer = top.
When you put a piece on a deck, it gets sucked into the deck. Vassal renders the appearance of the deck by the top piece in the deck. If you put a poker chip on a deck of cards, you will see a deck of poker chips. The rest of the deck is cards, but vassal will render them as poker chips. If you think about it, how would vassal know if what you put on a deck belongs there or not? How is it supposed to know that poker chip should not be in that deck? It means you can’t put pieces “on top” of a deck because they will fall into the deck. You will need to either put the piece next to the deck or not use a deck and perhaps use a stack instead.