Some email messages are flagged or rejected as spam, but I'm not sure why. Can I check how Spam Assassin is applying this score?
You can use the following command to read the rules applied.
su cpaneleximscanner -c '/usr/local/cpanel/3rdparty/perl/532/bin/spamassassin -D < /path/to/message' -s /bin/bash
You can also use spamc to check by running the following command:
/usr/local/cpanel/3rdparty/bin/spamc < /path/to/message
Please note, that you will need to replace /path/to/message with the full path to the message to scan.