Background layers were not turned on and didn't show up.
I assume you are using a multipage menu as the popup. Only page 0 can have the background in a multi-page menu.
I would experiment with a smaller number of layers in a new project. By the time you got to the 46 layers, I suspect the Encore project may have been corrupt. This is an unusual error.
I'm not sure I understand what you are trying to do.
Yes, absolutely use John's suggestion if you are not already.