Ah, its 3am and I cant even concentrate properly. This needs to be up in 5 hours.
I have migrated around half of the users from 2003 to 2010 and most of them have the old "Unable to delete source mailbox" error.
Cleanup Agent gets rid of all but 2 of them, which are stuck on the 2003 box as 0 items and 7KB.
I have tried the Limits things, setting the retention to 0 days. And doing Mailbox Maintenance.
By far the biggest issue is even mailboxes on the Exchange 2010 server are unable to be opened by Outlook.
Outlook just says the default set of folders cannot be opened. Autodiscover testing completes fine. Right Click and Connection Status shows only directory connected.
I can access the successful mailboxes via OWA and I can send/receive from there too.