Drush missing the "provision" and "Hostmaster" commands
Have had similar issues with this in the past,

How many instances of drush is there on your server? In my case I had a drush 3.3 version in /usr/share/drush and the aegir 4.4 version (with provision and hostmaster commands) in /var/aegir/.drush

In order to get drush to work, I had to alter the path for the aegir user to include /var/aegir/.drush first

You can always tell which version of drush you are using by running the command

which drush