Resolution:
When working with outbound EDI documents, a situration may be encountered where repeating separator do not get generated in outbound EDI documents, even though the XML is correct going into BC.  Also, when the XML is run against EDICONVERT, the EDI is generated correctly.

This is because EDI validation is not turned on for the Trading Partner for the outbound document.  To correct this, edit the trading partner, and under EDI-X12 Protocol | General | Outbound , check the "Enable EDI validation" box and save.  This will cause the separators to be generated correctly.