I stumbled over the same problem and discovered that I created the object entities (the ones in your second microflow) not correctly. Judging from the pasted screenshot, you have the same issue.
To fix it, you need to also create the associations between the objects e.g. from the JSON_object to the Root object. You can do this by creating a new member in the objects, see screenshots below.
I have turned the debugger,break point and variables pane on to debug the microflow. Seems like I am missing some steps while creating JSON structure mapped data structure.
Can someone share the microflow steps (also mapped export mapping, so that I can compare) needed to create this structure for PIE chart?