Layers Dropping out during print, Flatten?

To make this Brief, I work in PrePress. I recieve lots of Artwork from designers, etc.

I am having an issue with the PDF being printed, and Certain layers, and Text, Dropping out during print

So far the only way to fix this is to Rasterize the PDF- Flatten it to a JPEG at 600dpi, I dont believe this is the best method.

Does anybody else have this issue?