I have recreated the problem as the title states. I have a div that has a zoom and a Draggable item inside it. On zoom = 1 everything works great but if you change the zoom the Draggable position is out.
While using jQuery-UI Draggable I was able to fix the issue by the following code:
var zoom = $("#main").css("zoom");
// zoom fix
ui.position.top = Math.round(ui.position.top / zoom);
ui.position.left = Math.round(ui.position.left