[airhead83]

There's a slim possibility the wire delivering the 12v to the fan may have a bad connection or a 'close-to' break in the wire... causing the circuit to drop below 12v needed when it's under the load of the fan. Try hooking the wire back onto the fan as it would normally be, and letting the engine get back up tp temperature.... then check the voltage at the fan's connection to see if voltage is close to 12v... or drops .
If the voltage drops considerably.. It could be a bad connection or wire. OR... the radiator fan may be going bad and dragging ... A dragging fan motor would put an extra strain/load on the circuit. I'd be willing to bet you used a larger jumper wire than the bike's wire, A larger jumper wire could possibly carry the extra load of a dragging motor... and not drop below an acceptable voltage to turn the fan.
That's all I got. Good Luck.