The set up of the MSD native sync differs from the SFDC one in a few important ways. One of them is that you first execute your initial sync with the standard objects only and after that sync is done, you can configure the custom entities you want to sync. One really annoying consequence of this sequence is that there is no "initial sync" for the association of your leads/contacts/accounts with these custom entities. Only if there is a change to the custom entity for a person or account is that link set correctly.
As this starts you off on an incomplete representation of your CRM database, it would be great if this could be fixed soon.
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