Cloning works, but migrate doesn't | community.aegirproject.org

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My main site has 60k nodes, loads of contrib and custom modules, and four features. When I try to migrate it to a new platform, it has loads of errors with content types saying:

WD php: Table 'qubedevaroqcom_0.node_field_instance' doesn't exist query:
SELECT * FROM node_field_instance nfi
LEFT JOIN node_field nf ON nf.field_name = nfi.field_name
WHERE nf.active = 1 AND nfi.widget_active = 1
in /var/aegir/platforms/20120411_qube_a/sites/all/modules/contrib/cck/content.install on line 187.

Eventually, there are three task lines

Finished performing updates
Command dispatch complete
Peak memory usage was 50.25 MB

Followed by the trusty Drush was not able to start (bootstrap) the Drupal database and could not bootstrap drupal after updatedb.

This error message has a long history, some of which is here: https://drupal.org/node/486590

If I clone the site, however, it works fine.

The platform upgrade has all the same modules (and versions of them). The the only difference in platforms is that the old one is running Drupal 6.20 and the new platform is running 6.25.