OK, that helps, I can see the behavior now. It looks like a bug, but we'll have to look into it some more. It doesn't happen for documents, but it does for document shortcuts.
As a workaround, you can change the starting rule to use the entry not the parent. Then at the top of your workflow, add a Find Entry by path and set it to the %(Entry Path). Then add a Change Starting Entry and set it to the entry generated by Find Entry. The effect will be the same as your current configuration, but you will have the right entry and ID.