After transition/migration to Exchange 2007, your mails are going directly to ‘Deleted Items’ bypassing the Inbox. You have confirmed that a rule is not causing the issue. Probably the issue is that autobooking is set on your mailbox.

How to check:

Get-mailbox alias|get-mailboxCalendarSettings|fl AutomateProcessing
Example:  Get-mailbox johnd|get-mailboxCalendarSettings|fl AutomateProcessing

AutomateProcessing should be set to AutoUpdate for a user mailbox. If it is set to AutoAccept, run following script to correct the issue.

get-mailbox alias |set-mailboxCalendarSettings -automateprocessing:AutoUpdate

Re-Run: Get-mailbox alias|get-mailboxCalendarSettings|fl AutomateProcessing to confirm. It should give the following output this time.

AutomateProcessing : AutoUpdate

Worth a try.

— Thanks,  Jinesh.

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