Found a simple work around to fix the window layout error when creating new unity projects. The saving states which manage the current and last window editor positions seems to be corrupting. To work around this we need to rename two files, so that Unity may recreate using the 3d scene graph objects.
cd ~/Library/Preferences/Unity/Editor-5.x/Layouts/default mv LastLayout.dwlt LastLayout.dwlt.bak cd <project_dir>/Library mv CurrentLayout-default.dwlt CurrentLayout-default.dwlt.bak
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