When adding source Exchange organization it's required to specify single domain for enumeration purposes. As a result only recipients from one domain are enumerated. Is it possible to see all the mailboxes from entire Exchange organization?
During enumeration please specify FQDN (Fully Qualified Domain Name) of global catalog server, for example \\Server.domain.com and select "Use Global Catalog for Enumeration" option below. This will ensure that all mailboxes are enumerated.