Getting Component from javascript to C#

Hey guys i am making an FPS Game and i am using the First Person Controller Prefab unity provides me with. Unfortunatly it contains a script named CharacterMotor.js (which is a javascript, definitly) and regulates the movement. Furthermore I developed an animation system based on the movement for example when the velocity of the CharacterMotor is larger than a number then a boolean called Running comes true so my animation is being played. I dont know what happend when I updated my Unity3D to the latest version 4.3.2 but from now on my line of code doesn’t work:

public CharacterMotor CharMotor;

as a result I cant access it and my other lines of code which changes the boolean to true doesn’t work eather. If you noticed I used the declaration of the script which exists in my Standard Assets, but from now on it doesnt work why? :\

Well you can only access js variable from c# if the js file is in the standard asset folder.

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Updated Unity Scripting Reference link : Unity - Manual: Special folders and script compilation order