Email is missing in Exchange 2000

I am currently working on an Exchange 2000 --> Exchange 2007 Cross Forest Linked Mailbox Exchange Migration (phew)....

At the moment, I have done the following:
- Used ILM FP1 to import GAL from one side to the other and vice versa.
- Used InterOrg to replicate Free/Busy and public folders
- Implemented Windows 2003 Domain Extension in legacy domain
- Used PFDAVADMIN to export and import Permissions

I currently have a problem when sometimes, an email would come into the Exchange 2000 Organisation from it's SMTP Server, I can see that email gets delivered to Exchange from SMTP logs on Exchange, email goes to several recipients yet one user cannot find that email!

Alas, that email would be found in Deleted Items.  On one occasion the user , (MD was only using Outlook 2007). On another occassion, it was using Thunderbird via IMAP and Outlook 2003.  The actions that I have done tilll now do not justify automaticly deleting email.

What could be the problem?
stuvstuvAsked:
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Manpreet SIngh KhatraSolutions Architect, Project LeadCommented:
If there is any rule that is dooing that or the mailbox is set to be an Autoaccept Agent. As AA uses the same funda of reading and marking the mail for deletion.
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stuvstuvAuthor Commented:
the mailbox is a user mailbox, and does not have any rules to delete items.
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Manpreet SIngh KhatraSolutions Architect, Project LeadCommented:
Is the mailbox on Exchange 2000 or 2007 ?
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stuvstuvAuthor Commented:
The Mailbox is Exchange 2000.
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Manpreet SIngh KhatraSolutions Architect, Project LeadCommented:
Humm .. because if the mailbox is on Exchange 2007 we could have run a command to verify some info.
Is there any delegate or mobile sync that he uses.
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stuvstuvAuthor Commented:
Well Mobile Sync is only supported on Exchange 2003, SP2.    I dont think he has anything enabled locally with the old ActiveSynch with Outlook over cradle.

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Manpreet SIngh KhatraSolutions Architect, Project LeadCommented:
Any AV or Thirdparty Add-ons in Outlook of this user. Any delegates ?
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stuvstuvAuthor Commented:
resolving
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