[Read this thread][1], submit a bug report. [A similar issue was fixed for 5.1][2], this could be the same or similar bug.
[1]: http://forum.unity3d.com/threads/z-sorting-problems-with-nested-canvases-in-unity-5-1-0.332615/
[2]: https://issuetracker.unity3d.com/issues/upgrading-project-to-5-dot-1-no-ui-elements-appear-in-scene-view
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