Warning message occurs when gathering information for mailbox servers: "The following mailbox object could not be stored in the database as it could not be associated to a store on the given server."
There is code in the mailbox gathering that looks at the Message Store property to see if the given server name is contained in that DN. If not, this warning is logged. This message indicates that a given mailbox could not be associated to a store on the given server. This check is done to ensure that a mailbox is properly associated to the given store on the given server. This check was put in as there are problems with Exchange running on an Active/Active Cluster, where during failover a call to one virtual server's mailbox would return all mailboxes from all virtual servers.
Deleting the orphaned mailboxes will correct the problem.
A Feature Request has been created (CR0129705) to generate a more appropriate warning indicating that the mailbox is not properly associated to the Active Directory account and may be an orphan.