PO AutoSource not utilizing item substitution?

I have the enable Item substitutions checked on the purchasing definition including PO Sourcing. On the Substitute Item page at the Set ID level I have Use for Procurement set for Automatic Substitution, and the information is copied down to the IBU's. If I create a manual Req or PO with the Item being substituted I get a pop-up that states it is being substituted and places the Sub item. Yet when I bring in a req through req loader with the item being substituted, and then run PO Auto Source, the sub item does not replace the item to