Not sure if this is a bug or intended behaviour. When opening a Deck window, if you do not have any cards in the deck (such as for a discard pile), the “Reposition stack” button is greyed out. This means that you cannot position the deck on the board with this button. To get around this, you need to add a card to the deck and then the button becomes available to reposition the deck on the map.
It seems to me that you should still be able to use this button even if there are no cards in the deck as the x, y, width and height of the deck are already defined in the deck window.