1. SpamAssassin noi longer Prepend Subject Line even though I told it to in local.cf 2. Spam score mismatch in headers. 3. Spam gets delivered as it is but Spamassassin report was send as an attachment instead of the other way around!
for 1 and 3: You are using mimedefang, any markup options you place in local.cf are irrelvant. Mimedefang does it's own markups, and it's mimedefang you need to configure, not SA.
For 2: can you be more specific about this? what kind of mismatch? Are you getting an X-spam-status with a different score than the body report? If so, make sure you're not scanning mail twice. (ie: make sure there's no SA calls in procmail if you're using mimedefang)