Whenever you instantiate a Custom HTML Prompt, a drop-shadow circumscribes the window. You can avoid this by setting the Transparency flag, but then the visible items have a drop-shadow.
However, the drop-shadow is only applied to objects present during instantiation. So, if you delay all your drawing, nothing will have a drop-shadow.
You can do this with pure CSS (and then add a div tag in the HTML with this class selector):
.divbox {
width: 60px;
height: 60px;
background-color: #ff6699;
animation: 1s fadeIn;
animation-fill-mode: forwards;
visibility: hidden;
}