Which configuration is loaded after sa-update

I had a similar issue with response time, until I found out that the SpamAssassin database requires some minimal ongoing maintenance. Are you issuing

sa-learn --force-expire

on a daily basis? It could be that a lack of maintenance has made the database unweildy and it needs to be "trimmed up a bit". Try placing it in a daily cron job and see if the response is better on the next sa-learn run.

I have recently upgraded the mail server to a new CentOS 7 server (from CentOS 6) that is doing nothing but email and DNS. The previous CentOS 6 server was also running several websites on Apache.

I'm not sure what I'm doing differently that is causing bayes to show up in the Mail Headers as a test that was run, but it appears I have Bayes fully configured. Here's how I'm doing it:

As before, I'm running Postfix with amavisd-new being used as the primary Virus and Spam scanner. amavisd-new then hands off to spamassassin.

Postfix is version 2.10.1 from the CentOS Plus repository, amavisd-new is version 2.10.1 from the EPEL repository, and spamassassin is version 3.4.0 from the base repository.

spamassassin's config file is as follows:

[root@mail ~]# cat /etc/mail/spamassassin/local.cf 

    required_hits       5
    report_safe         0
    rewrite_header Subject [SPAM]
    razor_config /etc/mail/spamassassin/.razor/razor-agent.conf
    use_bayes       1
    bayes_path /var/spamassassin/bayes
    bayes_file_mode     077
    auto_learn      0
    use_razor2      1

And now, my mail headers do indicate the bayes test is being run:

X-Virus-Scanned: amavisd-new at developcents.com
X-Spam-Flag: NO
X-Spam-Score: 5.129
X-Spam-Level: *****
X-Spam-Status: No, score=5.129 tagged_above=-999 required=6.2
    tests=[BAYES_99=3.5, BAYES_999=0.2, DKIM_SIGNED=0.1, DKIM_VALID=-0.1,
    DKIM_VALID_AU=-0.1, HTML_FONT_LOW_CONTRAST=0.001, HTML_MESSAGE=0.001,
    MIME_HTML_ONLY=0.723, MIME_QP_LONG_LINE=0.001, RDNS_NONE=0.793,
    SPF_PASS=-0.001, T_REMOTE_IMAGE=0.01, URIBL_BLOCKED=0.001]
    autolearn=no autolearn_force=no

Unfortunately, I'm still trying to get a handle on the spam, as most of the messages are still coming in under the radar (with a score of 6.1 or lower), but I'm making a lot of progress.

For what it's worth, this is slightly off topic, but I recommend the following RBLs in Postfix main.cf as a part of the smtpd_recipient_restrictions definition (note that you'll need to register before you can use a couple of these lists):

reject_rbl_client zen.spamhaus.org,
reject_rbl_client bl.spamcop.net,
reject_rbl_client b.barracudacentral.org,
reject_rbl_client dnsbl.sorbs.net,
reject_rbl_client cbl.abuseat.org,
reject_rbl_client dnsbl-1.uceprotect.net,
reject_rbl_client dnsbl-3.uceprotect.net,

Hope this helps someone.