Think I've fixed it!
I changed the line in spamassassin.master.rc to read
#| {SPAMASSASSIN_PATH} --prefs-file={PREFS_FILE}
| /home/admispconfig/ispconfig/tools/spamassassin/usr/bin/spamc
then did an sql query to set all users to have u = "y"
and changed one user's settings.
Now it all seems to be working again
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