Signed messages not appearing properly in Mail on 10.11 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?
I use S/MIME extensively also, and have not seen this behavior in ElCap. I would try the following:


Rebuild your mailboxes. This will update the index metadata to point to the right messages, and is relatively painless to do (though if on a platter drive, possibly time consuming.)
As you suggested, delete your plists.