On the system affected, I cannot visit the "Manager" page under any the apps except search. I tried to visit the "manage apps" link which is under the manager and this time the page fully loads however the error message I get is (red bar):
There was an error retrieving the configuration, can not process this page.
Followed by a standard Splunk error:
You do not have permission to access the configuration for this page.
This works fine when visiting while in the Search app.
We went about trying to recreate this behaviour, and decided that the only way those errors could occur is if the permissions on the 'Manager' pages themselves aren't present. Those pages actually live in the 'search' app and the permissions are controlled by files in $SPLUNK_HOME/etc/apps/search/metadata.
If you looked at your diag, you may see that you are either missing the default.meta file and only have a local.meta file in there or, the default.meta file is present but the content has been altered somehow. default.meta is the file that exports the page permissions to the other apps.
If you changed the 'search' app via the Deployment server, tha might be an explanation as to why it disappeared, as it should be present when Splunk is first installed.
To restore it, just extract the file from the package tarball, copy it to the correct location and restart.