When I updated to XPA, I also had problems with some images overlapping others.
It was specially clear during combat, as some battler where above its window, but below the border of such windows. And they appeared above the text of the menus, hiding the letters of what you were selecting.
I had to make some modifications to my scripts.
Regarding XPA, I had to edit [XPA] XPA_Window -- def _update_z
I changed the values of the background and the border until it worked.
After that I had to make some strange changes in my project. I even had to modify some viewports in order to make everything appear where it should (I know I tried creating new viewports, but I can't remember if that was a solution or just something I discarded), so I don't really know what I did or where, so I can't be more specific
Maybe you can also fix your project making changes like that