Did you turn the option on for pdfs in the vault at the very beginning of its use or at a later point in time, as the pdf files are only created when the SolidWorks drawing files are checked into the vault it doesn't create a pdf for any other type of file. If the option was only turned on after some files were added to the vault these early files will not have a pdf.
You can use the SolidWorks Task Scheduler and the "Export Workgroup PDM files" function to create the missing pdf files in the vault.
Thank you for you reply, I cant remember if I turned it on later or not , but seems like the most logical reason for not having the PDF . I will check out a drawing and check it back in to see if that works.