This small edit will place x-spam headers back at the bottom of the original headers where god intended. I assume they changed this for a reason, presumably to maintain any cryptographic email signatures that include bits of header, so use this edit with discretion.
Find the file "PerMsgStatus.pm". Here's an example of where it might be: /usr/lib/perl5/site_perl/5.8.8/Mail/SpamAssassin/PerMsgStatus.pm Around line 967, change this: $new_hdrs_pre .= "X-Spam-$header: $line\n"; to this: $new_hdrs_post .= "X-Spam-$header: $line\n"; That's it. -Sean