hostmaster-migrate doesn't copy over settings.php

Hi,

I'm experimenting with Aegir to use as a hosting platform.

Here's my plan:
1) Install Aegir (hostmaster-install) with the default Aegir make file.
drush -y hostmaster-install --aegir_host=$DOMAIN --aegir_db_pass=$DB_PASSWORD
2) drush make custom hostmaster front end to new directory
drush make --working-copy $MAKEFILE $DEST
3) Update frontend to new install (hostmaster-upgrade). Enable my custom modules.
drush -y hostmaster-migrate $DOMAIN $DEST
4) Fiddle some code. hook_update_N. Test and decide to upgrade
5) Repeat from 2). Drush make and hostmaster-upgrade
drush -y hostmaster-migrate $DOMAIN $DEST

On the 2nd custom udpate, hostmaster-migrate isn't moving the sites/custom.dev folder- it's just putting the site in default.

What am I doing wrong? Any advice on this? Is there a better way?

Mike