We are just about done with our migration from Exchange 2003 to 2010. I have a user who has been migrated to the new system that is now out on medical leave. He has gone into OWA and set up his Out of Office notification. The good news is that an Out of Office message is sent, the bad news is that it appears to be sending an old outdated message from back when the user was on Exchange 2003, and not honoring the new message set up in OWA. The user has also tried setting this up in Outlook 2010 as well with the same behavior. I have a feeling that this is related to the old public folders (didn't they contain OOF messages?) still lingering around our Exchange org. Any ideas?
Try opening Outlook with the switch /cleanrules
Have they changed both messages?
Exchange 2010 has the concept of Internal and External messages, and when a mailbox is moved from Exchange 2003 to Exchange 2010 the OOF message is copied to both the Internal and External messages.
If the user only changed one of their out of office messages but neglected the other, that would explain it. You can check the out of office message values for the user with the cmdlet
Get-MailboxAutoReplyConfiguration username in the Exchange Management Shell.