When placing a Purchase Order using the filter "... Based on reorder levels and restock points, including customer specials *" only items from the Primary supplier appear on the order.
This seems to defeat the purpose of having a secondary supplier at all as you have to remember what needs to be ordered and add the item manually.
The workaround appears to be to "... Create the Purchase Order(s) for me based on all customer orders (from all suppliers) **" but this generates a huge number of orders that have to be manually removed.