Do you see them in ID with Overprint Preview turned on? What application are you using to view the PDF?
I do not see them with Overprint Preview turned on. The box is on the cover files. It shows up in mail preview and in iBooks.
Sounds like a viewer problem, rather than the PDF. Does it show if you use Adobe Reader?
Thanks for your responses. I was able to isolate it to the cover files. It appears to have something to do with the background layer / gradient. I changed from RGB to a swatch color, and the red box went away. However, now the cover file looks terrible in the Finder preview (Mac). The file itself is fine on Macs, iPads, iPods, and iPhones.
Lost about five hours to this one so far....
If anyone has had a similar issue and resolved it, I'd love to hear more.