From what you've said, can I assume this...
1. The IR LED is ok.
2. There is power on the 2 wires, at the end where the IR LED plugs in.
3, No matter which way you plug the IR LED into the 2 wires, it never lights up.
4. You have 2 other LEDs (IR or otherwise) that do light up when you plug them into the wires.
If I'm understanding this correctly, then I have to ask, how do you know the IR LED is OK? Have you tried hooking it up to a battery and watched it light up?
http://www.instructables.com/id/LEDs-for-Beginners/step5/If the IR LED lights up, but it doesn't light up when you plug it into the 2 wires (with power)... Then either the power from the wires, isn't making it to the IR LED (not making contact) or the power to the IR LED is turning off when you plug it in.