Steps to reproduce:
1. Open Project.
2. Open scene "Test Scene"
3. Click on the gameObject "Cube Prefab" in the Hierarchy.
4. Press the "Assign Variable" button in the Inspector tab under the "Box" component.
5. Notice the value is changed from the default "0" to "1".
6. Repeat steps 3 to 5 for the gameObject "Cube" to change it's value from "0" to "1" via the custom button.
7. Save the scene with ctrl + s
8. Goto File >> New Scene
9. Open the scene "Test Scene" again.
10. Click on the gameObject "Cube" and notice the value is still "1".
11. Click on the gameObject "Cube Prefab" and notice the value has reverted to the default "0".

Reproduced with Windows 10 (64 bit) on 5.2.1p3 (b7d18ab613bc), 5.2.2f1 (f5cc61d36935), 5.3.0b3 (b6181bece87a) and 4.6.9f1 (44099fd26189).