Where are you getting these PDFs? Literally every document in the world is unique. I just downloaded some Israeli tax forms and I have save them with no trouble. Obviously, your files are different. The PDF format itself is not what people think it is. It was designed to print - and absolutely nothing else. Virtually everything that people do with PDFs these days was a clever hack.
I can't begin to guess what the cause of this problem with your files might be. There are just too many possibilities for making a PDF that can be viewed, but not re-saved.
I think all you need to do is avoid re-saving the document. Instead of saving it from within Preview, just save the file from your e-mail to wherever you want it to live. Then, I recommend making it read-only so you can't accidentally overwrite it again. I have no idea what e-mail you are using, so I can't give you specific instructions. In Apple Mail, you could:
1) Drag the attachment to the desktop;
2) Choose "Save attachments" from the File menu;
3) <big sigh> Hover your mouse pointer over the middle faint grey line that separates the message headers from the message body to reveal (as much as a grey-on-white menu can be) the hidden menu and choose "Save all" from the "paperclip" menu.