I did manage to reproduce this.
(click for full-size image)
To reproduce it, I had to have the action selector set to Completed. Then I built a new project, put in actions A-E, selected action D, indented it, and got the result above. However, if I then switched the action selector to Remaining, the items were drawn in the proper order and relationship structure, so I think this is just a display bug in a corner case, and your data is fine. I'll send this in as a bug report with Help->Send Feedback as well.