When a Store or Administrative Group is selected and refresh is clicked, only the topology (not the mailboxes) will be refreshed. If a single Administrative Mailbox has to be added, in the Project Manager, right-click the Target Server and select "Add recipients to the EMW database" option.
If a complete refresh is required, re-add the Target Organization (without deleting it) and verify that "refresh exchange topology only" option is unchecked. This will refresh all Administrative Groups, Servers, Stores and Mailboxes on them automatically.
NOTE: Refreshing this information was changed in EMW 3.6 and later, for more details refer to Solution 10395 - "Quick Addition of New Mailboxes, Groups, and Stores in Exchange Migration Wizard 3.6":https://support.quest.com/SUPPORT/index?page=solution&id=SOL10395