Hi ncc,
The 'consolidate' option is simply to merge multiple sales orders for the same item into one line on the Auto-generate screen. This shouldn't have an effect on what you are trying to do.
It appears that the auto-generate function is grabbing all items on the grid when actually creating the PO, not just those selected (whether one or many). This is not how the process should be working as per documentation and for the confirmation screen you get, and I don't believe you are doing anything wrong.
For now, after doing the auto-generate and the two items are loaded for ordering, use the Delete button to remove one of the items from the generated grid and create a PO for the other item. Then repeat the process for the 2nd item.
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Regards,
Softrak Tech Support