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I may be wrong, but I'd suspect it's the ground. I think the reg/rec unit grounds via the mechanical mounting of the unit, and the extra wire should also go to ground. I'd suggest you wait for additional input before taking what I said to heart, though.
What sort of reg/rec is it?
 

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If you google eline coil, you will get some good links on Thumpertalk.

The yellows are positive AC, and the red is a common negative AC.

I also learned that many 'float the ground' (do not ground the coil) because the ground is actually an AC waveform and it positive and negative peaks, just opposite in phase from the yellow leads. If you ground AC to the frame, it may short out the battery or flicker your lights.

I have a Shindengen FH001 regulator/rectifier, it is used on the Yamaha FZ1 and some other bikes. I think I will feed in all three wires as this as I have read that the unit is FET type, electronic which is different from the shunt type reg-rect. units which mainly dissipate the heat - to condition the AC into DC.

The Shindengen FH001 should be able to take all three leads into it. Here is a wiring diagram for it

http://www.shindengen.com/resources/content/1/1/1/1/documents/FH012 Data.pdf
 
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