The following actions will help troubleshoot missing signatures:
1. Check that the e-mail has been processed by the signature application
See (Crossware Mail Signature System Fields).
If these fields are not present, then the email hasn't been processed by Crossware Mail Signature.
The field MAIL_SIG_CONFIGNAME_APPLIED will tell you which configurations were applied.
2. Check to see if the email has been signed or sealed (encrypted)
Signatures will not be applied to signed or encrypted emails. See Check Email Signed Or Encrypted.
3. Check fields against the $Users view in the Domino directory
Check the the From and Principal fields against the $Users view, to see if there is a match. See (How the sender of an email is determined).