Good Afternoon Lucas.
When indeed you have configured EEM for AD/LDAP, then AD is leading.
Which means that every group to be shown in EEM, needs to be created in AD.
Since EEM only retrieves it's information from AD, once configured for such.
As per Iain's update, please do check whether you have defined the Application Groups within EEM too.
For EEM, login to application='Catalog' and check for existing groups.
You need 'Application' groups, not 'Global' groups to be defined in EEM, for Catalog to see those groups for permissions settings.
Kind regards, Louis.