Unfortunately, I have no idea why that's happening, and hopefully someone comes by with a solution.
However, I strongly recommend not using Global Variables at all. I used to use them, and it was nothing but headache after headache with all the issues I experienced.
It's much more reliable to store those variables in an FSM on a regular game object (a game manager or something similar), and access those variables via "Find Object" and "Get/Set FSM [Variable]." If you put that object in your first scene, and attach a "Don't Destroy on Load" action to one of its FSMs, you can access it from any scene in your game.
Good luck with your project, and I hope whatever you decide to do works out.