I had this and fixed it.
I had upgraded to Mountain Lion and my signatures in Mail were fine. But then about a week later, I got a new computer and used Migration Assistant to copy my stuff to the new machine. Upon opening Mail, I had all the correct Signature information in the Preferences>Signatures window, but nothing worked.
After lots of hunting, I found the Signature Folder. It's in:
Yourusername>Library>Mail>V2>MailData>Signatures
Looking at my previous setup (which works) I saw in that folder two types of files: .webarchive and .siganture
Looking in my new machine's Signature folder, I saw only the .webarchive folders, not the .signature folders
Since this was literally a clone of my previous setup to a new machine, here's what I did:
1. Quit Mail
2. In Problem machine, go to
Yourusername>Library>Mail>V2>MailData>Signatures
3. Move the Signatures folder someplace safe, but out of the MailData folder
4. Get the Signatures Folder from the working install (like a backup) and copy it to the MailData folder on the problematic machine
5. Start Mail on the problem machine
This worked for me. I don't know why Migration Assistant didn't copy the full signature folder, but this fixed it. It worked perfectly partly because I had just backed up with Carbon Copy Cloner and the very next day set up the new machine. I don't know where Lion or earlier versions of mail stored signatures, but the absence of the .signature filetype seems to be the problem.
Hope this helps