Are you using actions such as (open an attachment, or launch a document) for delivery of the PDFs? Or are you just trying to include as attachments and then using Go To Web Address actions to launch them?
Maybe we do not see them being used and they are not published with the course. I would like to know more about this can you tell me which course it is that is having trouble, and is it okay if I download and look at your course in our development environment?
Well, I am seeing that the attachments do publish out when I publish to SCORM and then download the zip file. My guess it the actions to launch the PDFs are not working because of the modality of how the course is running inside the LMS. Maybe it is not allowing new browser windows to be launched.
You might try changing the open attachment action to a Go To Web Address action, select new window, and then make it a lightbox popup. This should at least allow the PDF to be displayed so you can know if it the PDFs are being written out in the content area. I’m attaching a screenshot showing what I mean…