Reproduction steps:
1. Open attached project
2. In menu bar - GameObject/3D Object/Cube
3. Notice that Cube is added to the scene
4. Reimport assets
5. Try GameObject/3D Object/Cube again
6: Notice that "true" is printed in console

Expected behaviour: Editor scripts overrides an existing Unity menu items as soon as project is opened.
Actual results: It does not override existing menu item until reimporting the script.

Reproduced on versions: Unity 5.3.4f1, 5.3.6p8, 5.4.2p2.
Did not reproduce on Unity 5.5.0b9