Saving pdf attachment is no different from saving any attachments. You could start with this code:
MailMessage mm = new MailMessage();
// load the message or download it from server
mm.Load(@"C:\temp\mail-with-pdf-attachment.eml");
// save the first attachment
mm.Attachments[0].Save(@"C:\temp\attachment.pdf");
If you have trouble saving the pdf attachment, would it be possible to zip the original email and then send the zip archive to support@rebex.net along with the version of Rebex components that you are using?
It will enable us to check whether it is a problem with the component or with the email itself.