The Signature application is unable to process emails that are signed (a digital signature appended based on the contents of the e-mail to enable the recipient to tell if the email has been modified) or sealed/ encrypted (contents of the e-mail are encrypted).
The application checks for emails that are signed or encrypted, if so the application allows the emails to pass without adding a signature.
Signed Emails
Signed emails contain a field $Signature
Encrypted Emails
Encrypted emails contain a field $Seal