Menu not showing for 1 server of two cloned servers
After a heavy duty migration like that, I would try going through the standard Drupal debugging steps first:


Clear caches.
Re-save theme settings (admin/appearance/settings/mytheme).
Rebuild permissions (admin/reports/status/rebuild)
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.
Check the status report and error log at admin/reports.


Good to cover your bases before you start digging deeper.