There could be a few mistakes in this thread, unless the later bikes had some big changes. Here's how my '97 works:
The sensor which is fitted in the bottom of the water pump housing only drives the temperature gauge.
The sensor at the back of the cylinder head tells the ECU about the water temperature so it can apply the right map when cold/warm. This is an important item. At the same time the ECU reads this sensor it triggers the fan relay. So it's the ECU controlling the fans with input from the cyl. head sensor.
Since the gauge and fans are on separate sensors they can both do different things - the gauge reading could be wrong and the fans cut in at the correct engine temperature, or the gauge is correct and fans cut in at the wrong temperature. The latter case is more serious because it means the engine map and cold start will be upset.
When the bike runs at cruise in not too hot weather, does the temp gauge hold steady at about 1/2 way. If it does this suggests the gauge is OK. If the gauge is reading low say 1/4 when the fans come on, that suggests the gauge sensor in the water pump is faulty. Also if you feel the radiator header tanks they should both feel quite hot when the fans cut in. If they feel cool and the gauge reads 1/4 then the cyl head sensor sounds faulty.
Now for the scientific stuff. I removed both sensors on my '97 K1200RS when the motor was out of the frame and measured the sensor charactersistics. Yours is a later bike so you may not get exactly the same values. But some information is probably better than none so I've attached my results in table form. If you want the XL sheet, PM me. Notice that the two sensors have quite different characteristics.
One final variable is the water thermostat which should be fully open at around 85 deg. C.
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