No, it sounds like they're running into the same problem I had initially, where each layer of the document is being saved as a separate file (iun my case it was a one-page document with five or six layers). I'm not sure where the option is exactly, but I inadvertently fixed it by switching to one of the pre-set PDF export options and exporting the file, and then switching to Custom afterward, where I've had it set ever since, and it hasn't been a problem.

-- Ben