When upgrading to versions of 9.3 a false positive message indicating that the latest cumulative site update is not applied. This was determined to be caused by the installation utility not updating the ek_securityupdate flag within the web.config file. Min site installations of the same version should have the appropriate ek_securityupdate settings for a site.
Our engineering team is actively working on updating the installers to update this flag correctly. Currently the recommendation would be to confirm that your version of Ektron has the appropriate security update patch applied. The release notes for the cumulative security update list what versions the update is currently written for. The ek_securityupdate field in the web.config file can be updated manually until the installers are updated with the appropriate versions.