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After cloning an existing server instance and pointing the new one to the same database I've modified my hosts files to load the 2nd server with the same URL as the first one.

All is well except for the fact that on the 2nd server the navigation menu is missing!

Any insight onto what may cause two otherwise identical servers to behave differently in this fashion?

update: the menu in question is generated by the superfish module.

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After a heavy duty migration like that, I would try going through the standard Drupal debugging steps first:

  1. Clear caches.
  2. Re-save theme settings (admin/appearance/settings/mytheme).
  3. Rebuild permissions (admin/reports/status/rebuild)
  4. If you are using the Features module, double check that things are identical to the old instance. You may need to revert some features components.
  5. Check the status report and error log at admin/reports.

Good to cover your bases before you start digging deeper.

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