Are they all in fact PDF files or are they various different types? Can you read PDF and other files onscreen with the browser, but just can't download them (or have you only checked this out with files that cannot be viewed onscreen and can only be downloaded)? Have you ever downloaded or read a PDF file of any kind (not just manuals) to verify that isn't the problem? You have no problems downloading programs or updates? Can you download files that aren't manuals or do you also have problems there - you mentioned a DMV record - is that the only exception to manuals or have you checked?
Even if you don't have a PDF reader, the browser should still allow you to download the file (even if you can't read it once you've done so) - so I'm not sure what is so special about these files. Please provide a website link or two with files you can't download so we can see if we have the same problem or maybe learn more about what might be the cause.
Thanks!