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In my Docking/MDI application, if a document in the main workspace contains a Direct3D rendering area (which is actually contained in a WindowsFormsHost), and an AutoHide ToolWindow is expanded, it pops out *behind* the Direct3D. It does appear properly when the ToolWindow is pinned, and when the main document is not Direct3D, AutoHide ToolWindows expand in front of the doc, as expected.
Video: https://www.screencast.com/t/cP8Wr5ci