Because in JEMsettings global parameters owned venues were yes. I think The creator of earlier venues= superuser has an other ID than the new Superuser. So the new superuser is not the owner of the old superusers venues.
If you want these venues only for the new superuser, you must adapt the creator of each venue.
Testing JEM 2.3.0 beta3 local on clean latest Joomla (3.9.11) Protostar php7.3.8 (no mails)