Do you have any anti-virus or recovery software running on the SQL server?
Are you sure they are deleted and not just assigned to another user or linked to another Opportunity list?
Are they deactivated? That would put them into another view and appear missing to a user.
If someone is deleting records, it will be hard to pin down who it is. Starting with CRM 2011, records are immediately deleted from the database now, rather than marked and cleaned up every 24 hours.
If you know the details on a specific record that is missing, you could do an advanced find to see if really is deleted or not.
Jason Peterson