LTM - check if config was loaded from wrong HD partition during upgrade

Also if you insall the configuration but not make the boot volume active and you continie to do changes, after weeks when you switch the active volume, the new volume will have the old configuration, even if you select again to install the configuration before the boot. Install the configuration can be done one time after that you need to delete and again install an iso image in the volume to be able to do install the configuration.

If the missing configuration is only new changes this could be the issue.