Are you asking me?
In the text file the shapes are knocking out the background completely (and do it in a new file, too), and the seps preview matches what you see in the screen grabs above. I only have the ID file, but when I make a PDF from it the shapes are missing in Acrobat, and I can follow the procedure I outlined above to replace one or two images and they show up in the PDF (and in ID), but the others are still just knockouts.
Want to play with the file? If it's OK with the OP I'll send it to you.