I discovered the source of the problem. It's the sa-learn script that runs at 1:30 every morning.
30 01 * * * /path/to/sa-learn --force-expire --sync -p /etc/MailScanner/spam.assassin.prefs.conf
I was a real Linux newbie when I originally built the Spamsnake and I entered the line into my cron just as you see it, not realizing that I needed to change "/path/to/sa-learn" to the actual path. I changed it to
30 01 * * * /usr/bin/sa-learn --force-expire --sync -p /etc/MailScanner/spam.assassin.prefs.conf
Now if I run that sa-learn script manually, it creates the Spamassassin scoring problem. The script itself has now been running for more than 15 minutes and is still running.
Any help would be appreciated.