I observed the same behavior in a new Ubuntu-Server 18.04 install.
It is possible that this behavior is related to two instances of
Spamassassin running. Disabling the standalone Spamassassin ("systemctl
disable spamassassin.service") made this problem go away. I still can
see the spam check in the amavis logs, and now the headers show that
spam checking has taken place.
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https://bugs.launchpad.net/bugs/1708142
Title:
amavisd-new does not scan for spam
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