Routing messages marked as [Spam] to Maildir/.Spam

I am using Qmail-Scanner 1.25 and Spamassassin 3.1.8 which is the most
recent available of the 3.1.x series to Gentoo users. 

Using qmail, vpopmail, and qmail-scanner to invoke spamassassin. 

I am using verbose spamassassin mode, and am trying to get mails tagged with
rewrite_subject [Spam] to be auto-delivered to the Maildir/.Spam folder. 

The challenge is that I want this to be done site-wide, and for some reason
that I cannot tell, this no longer works for me. Meaning that it was
working, and I cannot explain why not any longer. Except that on Friday, I
needed to remove fprot from the qmail-scanner process. It was throwing some
nasty errors on my box, and when I recompiled everything, I've just been
getting no love at all. 

However, one thing that is of interest is that MOST of the [Spam] ends up in
the proper place. Some [Spam] slips by. The stuff that slips by is somehow
using the /etc/spamassassin/local.cf preferences. All the [Spam] that is
properly delivered to Maildir/.Spam is using my
/var/vpopmail/domains/%d/%l/.spamassassin/user_prefs file. 

What would be the cause of two different prefs files in use by the same
account? It's the weirdest thing. 

Qmail-scanner config options: 

./configure --spooldir /var/spool/qmailscan --qmaildir /var/qmail --bindir
/var/qmail/bin --qmail-queue-binary /var/qmail/bin/qmail-queue  --admin
postmaster --domain ark --notify psender,nmlvadm --local-domains ark
--silent-viruses auto --lang en_GB --debug 1 --unzip 1
--block-password-protected 0 --add-dscr-hdrs 0 --archive 0 --redundant yes
--log-details syslog --log-crypto 0 --fix-mime 2  --ignore-eol-check 0
--scanners "auto" --install 1 

Spamd runtime options: 

-c -d -v -s local4 -q -u vpopmail
--virtual-config-dir=/var/vpopmail/domains/%d/%l/.spamassassin/ -H
/var/vpopmail 

Any help would be greatly appreciated, I have lost 3 days looking for an
answer but have just exhausted myself trying. Thanks.

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