Applying the upgrade upgrade-4.6-4.6.1 script to the database from the command line like so:
psql -f ./packages/acs-kernel/sql/postgresql/upgrade/upgrade-4.6-4.6.1.sql service0 > upgrade-4.6-4.6.1.log 2>&1
and then starting the service and doing the other two scripts from the package manager installer works fine.
