Hello JeffHarsh
Thank you for your post.
We are aware of this issue that you are facing and has been logged with our Product Development team.
This is caused by having committed items. Stock Alert - Select All is not including items which are = or > than the min restock number but have committed amounts.
What you can do is when using the To Do List if you select the lines manually the order will be created, items should only be missing if you use the Select All option. Otherwise, you could create separate purchase orders for items with committed amounts.