Why is these options not appearing on all not yet delivered sales order lines? The items are identical, sometimes it is the same item on different orders that both show and not show. It shows on items that are not marked as drop ship / special order items in some cases..

Do you have the feature Intercompany Cross Subsidiary Fulfillment Enabled?

No, not yet. We want to use it, but in the process of evaluating that function, I stumbled upon this situation

You have to have the subsidiary and inventory location set on the line item level for the drop ship link to appear