Adobe encore - Highlight button with image
Sounds like it may be some kind of a processing glitch.  Menus don't actually do an overlay when you mouse over them, they display a different image.  If you export one button with highlight and one without, you can specifically set the hover image of the button to be the one with the highlight.  You specifically have options for selected, unselected and hover.

If you need more detail about how to do this specifically, I can put together some screenshots when I get to my editing workstation, but I seem to recall it being relatively easy to find in the properties of the button.