a few possible reasons.
1: the fan doesn't work. take two small jumper wires and connect the directly to the battery and the leads on the fan. if it works, then...
2: your temp sensor has failed. remove the sensor and, while keeping it connected to the leads and with the key in the "on" position, try either putting a flame to it or immersing the tip in boiling water. if the fan comes on, then...
3: using a multimeter, disconnect the leads from the sensor and from the fan and test the wire for current. you could also just bypass the wire by jumping the sensor directly to the fan while leaving the wire connected and then following step 2 again. if it doesn't work, then...
4: with the key in the "off" positon and using your multimeter, attach the negative lead to the negative terminal on your battery and then touch the positive lead to a grounded spot on the frame. there should be absolutely no current. if there is a current (which will be small or will read as a negative (-) current), then...
5: check the entire electrical system for worn/damaged wires where the positive connection from the battery or any accessories has come into contact with the frame or any other grounds. this won't always stop a vehicle from running but it will cause strange and/or damaging electrical failures to occur. this is rare, however... at least by comparison to the problems mentioned in the other steps.
if none of this helps then i would have to say that you may just be riding either too short for the bike to get hot enough or you're riding in too cool of weather for the bike to get hot enough. i have a cbr 600 f2 and the fan almost NEVER comes on... even in 80 degree weather! it usually only comes on if I'm at a red light for too long in the heat and after riding at least 15 to 20 minutes. naked bikes ESPECIALLY are able to stay cool under normal riding conditions.
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