A changed boundary marker (which does not affect the message signature), a two-line header moved onto one line, and a deleted header (presumably because the
default transfer encoding is 7bit.)
Now, one might argue that a better design for MIME would have been to sign only the message and not the headers, but that would open the way to all sorts of devious attacks involving changing the header, and defeat the entire purpose of the S/MIME standard. So there we have it.
If I get some time in the near future, I'll look into the source and see if I can't find a simple way to keep Courier from rewriting the headers.