I suggest you contact Doobox directly. Maybe even ask them to look at this thread.
The error in your uploaded grab seems to be associated with a graphics file in Stacks. Have you/had you moved any graphics files around 'manually' outside of RapidWeaver? That might possibly cause such an error, perhaps.
If you post the URL of the page with the PDFs here, we can look at it and see if we can maybe find out why you're unable to download them.