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It seems like i solved this issue: I had the SceneVariables Script on a prefab in the scene that had unapllyed changes. After i removed that prefab and added the SceneVariables Script to an new empty Gameobject it works. BUT is seems to work only when i change Variables in the Inspector that displays the GameObject  - not when i do changes in the veriables Inspector. Still seems strange but i can work now.

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