Steps to reproduce:

1. Open the attached project
2. Open 'default' scene
3. Notice there are two objects, that have the RigidBody.position changed in the script and right after that, the objects are re-enabled
4. Play the scene
5. Notice that objects transform position is not updated, but the position of rigidbody is (you can check that by outputting RigidBody.position and Transform.position to the console)

Workaround: Change the position of the object using Transform.position instead.

Reproduced with: 5.0.4f1, 5.2.3f1, 5.4.0a3