Missing menus in Enterprise Security?

[BrendanCO]

Hello! I've had a few successful installs of ES but this newest install only has one domain under "Security Domains" (Identity).  Security Intelligence is missing menus as well. Most of the Data Models appear to be populating correctly and are accelerated. I'm getting good menus in Infosec. I've tried to reinstall it twice. I've also looked for any TA nav menus that may be overriding and I don't see anything.
Any thoughts as to where to continue troubleshooting?

[BrendanCO]

So to add to this. I suspect there is something that is overriding the menus. I've checked all the TA's and can't seem to find anything. To be sure, I zipped up the entire SplunkEnterpriseSecuritySuite folder from a working instance and overwrote the whole folder on the non-working instance (yes, I stopped the service and then restarted after the unzipping) and I got the exact same results. Missing menus. 
I've also checked the Audit and the config settings in SE, and don't see anything out of the ordinary there.