Automation does not add any VBox. This Vbox is from your application only. Check the complete identification of this component. The Vbox need not be in the application hierarchy of the textArea. There is no relationship between the Vbox and the control you would like to interact.
It is the fact that this container is overlapping the control "physically" not hierarchically.
Details of this issue are addressed in the blog below.
http://ranikumar.wordpress.com/2008/04/02/automation-issues-controls-non-clickable
Hope this helps.