If you are receiving problems with emails containing PDF files, there’s actually two different filters that  could be affecting this. They can be disabled by editing the SpamFilter.ini file. These settings however are global, and cannot be configured for specific domains.

Blank emails that contain PDF attachments only can  be allowed to pass by removing the “*.pdf” value from the line below. Please  do not remove the entire line, just remove the vales after the “=”  sign.

;SpamFilter can  block emails that contain only an empty, blank body and one of the following  attachment. Clear the list if you don't want to stop such emails. Specify  multiple attachments separated by  commas
BlockBlankEmailsWithAttachments=



You can disable the option to scan within PDF files for spam image signatures by setting the following value to zero:

;Specify the max number of pages a PDF document must  contain in order to be scanned for spam signatures. The scan will be skipped  altogether if there are more than this number of  pages
SpamPDFMaxPagesToScan=0



Please note that the latter PDF filter that scans for images within PDF files is related to the "standard" filter that scans for images within emails. If you disable the image filter for a domain, this will also disable the PDF image filter (but not the one that looks for empty emails with a PDF attachment only - this one is a global filter).