A solution... for now....
My problem was specifically with trying to work with PDF files, as a work around instead of using the data type of "File" for this, I have just made the data type "Image" and it actualy seems to work. Of course you don't see a thumbnail of the file, it just remains blank (no feedback at all when viewing the entry in the popup) but everything else works fine amazingly.
Hopefully that will help anyone at least get the functionality working for their site until we find out what the real issue is.