I found the registry keys, so I can confirm that the percentage setting is enrolled to the servers.
HKLM and HKCU registry hives: SOFTWARE\Policies\Microsoft\Cryptography\AutoEnrollment\
Keys: OfflineExpirationPercent, OfflineExpirationStoreNames=MY and AEPolicy=7
So, why do I get event ID 1003 when certificates are on 50% lifetime?