SD -06 temperature indicator issues

I tried to search answers to my small but annoying problem but couldn't find any so i start on new topic. Here's what happened. I put V&H slip ons to my Duke remapped ecu with some basic set up and plan was to make more specific mapping on dyno. Everything went fine until it was time to do 15 min reset. So i left my bike on idle and went inside but when i came back the temperature indicator was flashing and warning light was lit up. So i assumed that warm day and long idle has done its job so i took a little cooling drive nearby but it didn't solve the problem considering the warning lights but i checked by IR thermometer that engine was at normal temperatures. Here i have to say that i think it was not overheating at any point beacuse there was no steam or water coming from the system. After short thinking first thing i realised was that the cooling fan was not operating and i have to repalce it. I think it should be different issue but dont know if it has caused this problem. Maybe some too high peak current or something. The fuse of the fan was burned althought. I have make some measuring and temp sensor seems to be working and ecu shows right temperatures when checked with Tuneecu. Bike works fine otherwise but now the situation is that you dont have to even start the bike just turn the power on and wait like one minute and indicator starts to blink and warning light stays lit. And bike in question is 2006 with older style speedometer. It seems to be that in finland i am the only one with this kind of problem so could anyone help me in here please?

Check engine temp sensor and wiring - likely to be faulty sensor and/or short circuit.

Comrade: My reasoning is that because tuneECU knows the correct temperature the sensor and the lines to the ECU are fine. Here I assume that tuneECU sees the temperature rise from cold.

From memory there is a line from the ECU to the instrument. It passes through a 12 pin connector in the headlight (blue and orange). I doubt that it is the connector although it would be a good idea to check. From there it is straight into the instrument cluster via a connector in the back of the instrument but I doubt that is the problem if everything else is Ok. I wonder if the warning light is trying to warn you that the fan is dead. It's not giving you a F1 error code of 12 (blink pause blink blink) is it? If so the sensor is too high or too low.

The only other suggestion I can make is to try to borrow another instrument and plug that in.

The wire on the sensor is know for bad connections. It sits behind the front cylinder on the left hand side of the bike.
Pull the wire of and clean the connector and the male bit on the sensor. Put a bit of lube to keep it from going rusty (like copper slip).
If that doesn't fix it you have to do as suggested above and check the wiring.

OK, and thank you for these advices so far. Problem must be between ecu and (or inside) instrument because when engine was warm temperature shown in Tuneecu was showing something like 85 degrees celsius and next day in my carage it was quite the same as air temperature. And there was no error codes. I have to specify the cooling fan issue which i told about. Old fan was almost completely jammed so assume that when it tried to rotate it was generating quite high current. So i am afraid that it might have distroyed something inside instrument. But i have check the wiring first and hope for best. After i checked oem parts and ebay pricing it might be good time to update the headlight/instrument cluster to some after market system if i have to buy new items.

After searching some possible wire/connector issues i am begin to believe that the problem is in the instrument. Just to be sure and excluding every possible thing and this might be stupid question but is there any possibility that remapping the ecu with Tuneecu could do something like this?

How have you discounted the temperature sensor, connectors and wiring (lhs of rear cylinder not rear of front cylinder)?

I measured the temp sensor and the readings seemed to be quite right in different temperatures and ecu seems to know right temperature.