Thanks so much Furry, that was worth a try but didn't work.

I've noticed two things since: That the “ghost” square does not simply cover the area of where the initial square was but that it covers the area that the square and the drop shadow would cover (had they not been rotated). Scouring the Net I've found similar instances of ghosts appearing when people printed out documents. In my case, the ghost is only visible on the high-res PDF, not on the InDesign document and not visible when I do an overprint preview (View >> overprint preview). I don't have a printer here so can't check it if would print.

Incidentally, the photo is placed on a CMYK background with a 30% tint.

Thanks again