Reproduction steps: Unfortunately I cannot reproduce this now, but likely it was a combination of me installing/uninstalling various antivirus solutions (including KSOS beta). That being said, with all the other AV software (including KIS) nothing like this happened yet.
Actual result: Kaspersky's Certificate not installed. And the KES GUI overview shows various components not being active (those small green/gray LEDs that instead say on/off in KIS), but going into their respective settings then shows them as enabled.
Expected Result: Certificate being installed and GUI overview of settings on/off state matching each specific setting.
Before doing all the AV test installations/uninstalls I created a Windows Restore point to which I returned. Installing KES from that Restore point works as expected. So this is more of a "for your information" post, since I cannot replicate it now and all logs are gone already.