I'm assuming since you mention ESM and virtualization that you are running Exchange Server 2003 and Microsoft Virtual Server. It sounds to me like your Recipient Update Service (RUS) isn't properly stamping Exchange Server with the appropriate attributes. For more assistance, read Microsoft's article, How to troubleshoot the Recipient Update Service by using the application log in Exchange 2000 Server or Exchange Server 2003.
It could be that they did not logon as the user after creating the mailbox. I have noticed that I have to initialize the user account, by logging into Outlook Web Access or Microsoft Outlook first, in order to have the mailbox show up in the ESM. I hope this helps.
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