Unity doesn't open a custom editor window that is a part of a custom layout when opening the project or changing the layout in the editor

To reproduce:
1. Open the project attached by the user
2. Open the custom EditorWindow by clicking on Window > Level Building Assistant
3. Save layout
4. Close and open Unity again with this layout or change the layout in the editor
5. Observe that Unity has not opened the custom editor window that was a part of the layout

Expected: custom editor window opens when changing the layout or launching the project
Actual: custom editor window does not open when changing the layout or launching the project

Notes:
Trying to change from default layout to custom on Unity 5.4 crashes Unity causing a System Exception.

Reproduced on: 5.5.0b3, 5.4.0f3, 5.4.1f1, 5.3.6p5, 5.2.5f1