Hi Swampy,
I haven't experienced this, but have looked at totally non-functional fans. A good place to start is the coolant temperature sensor. Section 6-4 and other sections of the service manual talk about it. They state it is quite a fragile flower!
Temperature sensors themselves are components which give decreacing resistance as measured across their terminals as temperature goes up. So if you have a decent multimeter you can test this at different coolant temperatures..
A guide to this for cars is here for instance,
http://www.howstuffinmycarworks.com/...mp_sensor.html
The temperature sensor should give out a resistance of 2.28 - 2.63 kohms at 20 deg C and this drops to 0.138 - 0.145 kohms at 110 deg C, so Yamaha say anyway..
If you were to remove the plug from the temperature sensor and make a good connection across the PLUGS pins with a 150 ohm resistor, (150 ohms = 0.150 kohms, so that = a temp over 100 deg C as far as the sensor output is concerned), I would expect the fan run normally as it would at high temperature. The plug would be seeing the same resistance as the temperature sensor would give..roughly anyway. I don't know if the engine has to be running or just with the electrics on, some systems will even run the fan when the key is out... BTW, good temporary electrical connections require pushing quite hard, (you will see this when you try measuring something with a multimeter, you wont get the correct reading just by touching the probes to the metal surfaces).
If this resistor test makes the fan work normally, then you have a bad temperature sensor, or the connection is not good between the sensor and the plug. You could try cleaning the connectors and refitting. Sometimes the wiring is broken and annoyingly intermittently works when you mess about with it! You can throughly check the sensor by removing it and sticking it in hot water and checking the temperature with a thermometer against the resistance at the terminals too, service manual describes this test..it will keep you busy if you do this..
A diagnosis of bmw K bike fan problems will give you a general idea of how these systems work, see
http://www.ibmwr.org/ktech/fan-diagnosis.shtml
If problems persist when the plug is seeing a 150 ohm resistance during test, it is likely a relay fault, my manual lists this part as,
ACM33211 M04/MATSU****A
You could try exchanging it for a known good one, or, if you sign up to be a xt660.com supporter then you can get the full service manual which details testing the relay. I don't know if you are comfortable testing electrical stuff, but just like the mechanical side, you have to start learning somewhere and it isn't as bad as it looks!
I strongly suspect the temperature sensor is on its way out, but you never know for sure till it's fixed!
Hope you get it sorted!