So after no pointers in the right direction I started breaking down the init.d for amavis and noticed that if the Binaries are not found that the init.d simply exit with error code 0.
I traced the binaries and saw that the although Ubuntu reported amavisd-new as installed the binaries were missing. I did an apt --reinstall amavisd-new which re-installed 1:2.11.0-1ubuntu1.1 and low and behold the mailfilter module started, after a manual service amavis restart that is..
Next another snag hit, when attempting to do a manual sa-learn for SpamAssassin, I was greated with failure. running the same sa-learn command with the -D option showed me that the amavis user did not have access to the spamassassin db in mysql
This was fixed using the following
GRANT ALL PRIVILEGES ON spamassassin.* TO 'amavis'@'localhost' IDENTIFIED BY '*******';
The password obscured by the asterisks was obtained from /etc/spamassassin/local.cf at the "bayes_sql_password" line.
Hope this helps someone else with this issue