If you supply 5V to your throttle's red wire, and ground to the black wire, then put a multimeter across the black wire and the third wire, you should see less than 1 volt when the throttle is not engaged, and about 4 volts when it's fully open.
If that's what you get from testing it, then the problem isn't the throttle itself.
If you can't measure 5 volts from pins in the controller to throttle plug, then the problem is in the controller or the wire.