If your organisation encrypts some of its email, you may notice that those messages arrive without a signature. That is deliberate, and in most cases you can have both.
Adding a signature means changing the message. An encrypted message cannot be changed without breaking the encryption, and a message signed with S/MIME is protected against exactly that kind of change: alter a single character and the recipient's mail app warns them the message has been tampered with. A signature is never worth that.
So when a protected message reaches Footer365, whether it is encrypted, S/MIME signed or protected by a sensitivity label, it is passed straight back exactly as it arrived. It is never opened, never delayed and never rejected because it is protected. Your audit log notes that it went through without a signature, and why.
Most encryption in Microsoft 365 is applied by a mail flow rule in your own organisation. If the signature is added before that rule runs, the recipient gets a message that is both signed and encrypted. Footer365's own rules are created at the top of your list for exactly this reason: the message goes to Footer365 first, comes back signed, and your encryption rule then protects it on its way out.
Two things keep that working. Keep your encryption rules below the Footer365 ones. And never add an exception for the Footer365 processed header to your encryption rule: that exception belongs on the Footer365 rule only, and on an encryption rule it would mean signed mail is never encrypted at all.
Protection applied in Outlook itself, such as S/MIME or an encrypting sensitivity label, happens before the message leaves the sender's mailbox, so no rule order can help. For those, the Footer365 Outlook add-in writes the signature into the message while it is being written, before it is protected.
The full detail is in Encryption, S/MIME and rule priority.
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