It may be necessary to check the file extensions of exported items in Archive Shuttle, in order to do that review the steps below.
The following SQL will show the file extensions of exported items for a particular container mapping ID:

DECLARE @mappingId int;
SET @mappingId = 2;
-- Get all items where is no file extension or is other then .msg
select I.ItemId, FE.Name FROM Item I LEFT JOIN 
    FileExtension FE ON FE.FileExtensionId = I.FileExtensionId INNER JOIN
    ItemRouting IR ON IR.ItemId = I.ItemId
WHERE IR.ContainerMappingId = @mappingId AND (I.FileExtensionId is null OR FE.Name <> '.msg');


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