Winshuttle output column order for a table (KNA1) should be the same as that of the SAP output of the table (KNA1).
Winshuttle output can be mapped to excel as requirement. Remap columns in the order of SAP export.
Screenshot of the SAP output
In order to avoid confusion, create a new script.
Do Not automap.
Under Map tab >> Mapper section, drag the fields on excel in the order of SAP export/ output.