Repro Steps:

1) Create a Page.
2) Drag a Button onto the stage.
3) Create a Template for the button, and edit its contents.
4) Wrap the pre-existing Content Presenter into a Grid, (whilst still conserving the existing RootGrid - so there should now be two Grids in the navigator)
5) Wrap the Grid created in Step 4), into a StackPanel.
6) Rename the StackPanel to a custom name ("MyStackPanel" works)
7) Change the ordering so that the Stack Panel is now under the RootGrid rather than under the Grid created in Step 4)

Observe how "MyStackPanel" has been renamed to [StackPanel].

Expected Results:
Layer Names do not change as a result of re-ordering them within the Navigator.