I do a lot of work with S/MIME and am very familiar with the standard and the software.
Since upgrading to 10.11 (El Captain), S/MIME-signed and encrypted messages have not been appearing as such in my Apple Mail App on my laptop. The same messages do show signed and/or encrypted on my iPhone.
I have never seen a problem like this. Any suggestions, other than reinstalling the OS or wiping out the Mail preferences?