Hi Guys
Figured this one out by my self, all I did was send the output of the init.d script to /dev/null and backuppc was happy.
#!/bin/bash
# This script starts up alfresco after a cold backup by backuppc
/etc/init.d/alfresco start > /dev/null 2>&1
sleep 20
echo "ALFRESCO HAS STARTED"
exit 0