By any chance, could that specific copy of the PDF be the result of a Find pulling up a found set of zero records? I realize you've said that they're "fine on your end" but that's the only thing I can think of. You'd need to either check this very carefully or include code in your script that uses get ( FoundCount ) to check for empty found sets in order to investigate this possibility.
Thanks for the reply and I wish it was something like that. The emails and PDF's are created separately and I have gone through each to check. I have managed to replicate the issue by sending an email to a webmail account and checking the same email in Outlook. The webmail version was blank and the Outlook version was fine. This leads me to think it is related to the PDF format or something similar. However, I am not convinced that it is only occuring with those using webmail as I think some of the recipients with blank version are using Outlook.