Sorry, I'm being stupid here... Why does it need to go on a fan header if it's connected to the case controller or is it simply there as an optional plug? Basically it has two cables coming from it, one 3 pin that connects to the fan controller and the 2 pin which isn't currently connected to anything yet.
Oh... Err... Umm... If it works without plugging the second lead in... Leave it and declare it a mystery

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