Spamassassin works but not with MS

[Stephen Lee]

I'm running MS 3.24-1 with SA 2.42 on Trustix 1.5/Perl 5.6.1. It appears
that SA correctly identifies spam but through some interaction with MS,
the message is not tagged as spam. Here's an example header:

X-Spam-Flag: YES
X-Spam-Level: Spam-Level SSSSSSSSSSS
X-Spam-Checker-Version: SpamAssassin 2.42 (1.115.2.14-2002-10-04-exp)
X-Spam-Report: 11.40 hits, 5 required;
     * -1.2 -- User-Agent header indicates a non-spam MUA (Mutt)
     * -0.5 -- Found a User-Agent header
     * 3.4 -- BODY: Claims you can be removed from the list
     * 1.0 -- BODY: Multi Level Marketing mentioned
     * 0.8 -- BODY: List removal information
     * 0.7 -- BODY: List removal information
     * 0.6 -- BODY: No Inventory
     * 0.5 -- BODY: Do it Today
     * 0.4 -- BODY: Claims you can be removed from the list
     * 0.4 -- BODY: Asks you to click below (in caps)
     * 0.4 -- BODY: List removal information
     * 0.3 -- BODY: Asks you to click below
     * 1.3 -- BODY: Spam phrases score is 13 to 21 (high)
     [score: 13]
     * 0.3 -- BODY: FONT Size +2 and up or 3 and up
     * 0.3 -- BODY: HTML font color has unusual name
     * 0.3 -- BODY: HTML font color is red
     * 0.2 -- BODY: HTML font color is blue
     * 0.6 -- BODY: Tells you to click on a URL (in caps)
     * 0.3 -- BODY: Tells you to click on a URL
     * 0.2 -- BODY: Includes a URL link to send an email
     * 0.7 -- URI: Includes a link to a likely spammer email address
     * 0.4 -- Subject has many exclamations
X-MailScanner: Found to be clean
X-MailScanner-SpamCheck: not spam, SpamAssassin (score=-2.5, required 5,
     AWL)

Here's a sample syslog message with debug turned on:

Oct 17 22:42:22 mail mailscanner[27826]: Scanning 1 messages, 8181 bytes
Oct 17 22:42:23 mail mailscanner[27826]: RBL Checks returned 0
Oct 17 22:42:24 mail mailscanner[27826]: SpamAssassin returned 0
Oct 17 22:42:24 mail mailscanner[27826]: Going to scan 1 messages
Oct 17 22:42:24 mail mailscanner[27826]: Commencing scanning by
sophos...
Oct 17 22:42:24 mail mailscanner[27826]: Completed scanning by sophos
Oct 17 22:42:24 mail mailscanner[27826]: Scanned 1 messages, 8181 bytes
in 0 seconds
Oct 17 22:42:24 mail mailscanner[27826]: About to deliver 1 messages

I'm not sure where to look. I've reinstalled SA as well as all
associated modules for MS and SA. Any other diagnostics I can run?

Thanks for your suggestions,
Stephen