@Jason think i've tracked down problem when you go into your images folder it gives all fanart a new prefix -01 at end of fanart name this cause LaunchBox to think there are 2 fanart images, the image you had set for the game or item in the respected platform and the now new image with the -01 prefix see below image:-
Used my background image for my media centre as you can see it renamed the fanart image from MediaBox.jpg to MediaBox-01.jpg, the same applies to the other platforms and only applies to the fanart images as have no screenshots, logo's etc or other images except box front images and fanart images to cut down on size in images folder.
As you can see the changes it made to names in ScummVm images fanart the same applies to all platforms