Also notice in both of my pictures on the left hand side you can see how the GFUI interpreted each…In the one photo it sees the cuts…in the other it does not.
@tim1724 pegged it… The file that has the multiples in it just has the bitmaps, it does not contain a separate vector cutline. (The blue line shaped like a rectangle with a tab at the bottom is part of the bitmap and it will engrave along with the text and numbers.)
Perhaps when you rasterized the file to create the bitmaps you accidentally included the cutting path as well.
(All you need to do is copy just the cutting path from one of the single SVG files over to the multiple file SVG, and then align it over each of the bitmaps, then save it again.)