Looked at this post:
Help dealing with spam
and saw it suggested to run sh -x zmsatrain for debugging.
Before I've run the zmsatrain as the installed cron job and the spamtrain.log showed a successful run with no errors, and have also run it standalone against a specific folder for a particular user and it also ran with out error.
Running sh -s zmsatrain yielded this:
sh -x zmtrainsa
++ whoami
+ '[' xzimbra '!=' xzimbra ']'
++ dirname zmtrainsa
+ source ./zmshutil
/opt/zimbra/bin/zmtrainsa: line 66: ./zmshutil: No such file or directory
Changing line 66 from this:
source `dirname $0`/zmshutil || exit 1
to this:
source /opt/zimbra/bin/zmshutil || exit 1
results in a successful run.
Now all three (cron job, manual run and sh -x zmsatrain) all run without error. Still no bayes score in the headers though.