Could you show us the piece of code that does that?

Ugh...i posted an answer to this like 3 hrs ago...I wish my account didnt get screwed up in the move to dev unity wtevr site.

boolean defaults to false..so if you create a new instance of an object that has the same script(unless declared otherwise) it will start out false (regardless of inspector-since the inspecter reference was to the parent and not this clone).

To fix

Simply say that this variable = true upon instantiation

public var myPlayer:Transform;

function ClonePlayer()
{
    var clone=Instantiate(myPlayer,myPlayer.position,myPlayer.rotation);
    clone.GetComponent(MyScript).variable=true;
}

please dont comment as the answer, so i get notification about a new answer. But, hey thanks OperationDogBird, your answer its true, now my gameobject work properly. Thank you very much