The fan is supposed to kick in at a particular temperature (i can't remember off my head the exact temp).. i've seen this with the diag tool connected and waited for the fan to come on. and once it brings down to particular temp, the fan shuts off.
Only variation i have noticed is a wee bit change in speed when the headlights are on vs off at idle (on older dukes). Apart from that there is no variable rpm for the fan.
You can go ahead and read thru the 'self study manual' for the ktm 390 (just google it/check the online manual documents it should be there). this will give you a better understanding of some of the workings of the bike.


There shouldn't be any fluctuation whatsoever, apart from using high beams with the fan running which would wee bit slow the fan, which is perceptible and normal. Under normal circumstances, the fan should perfectly wake up from its slumber when pricked upon, slowing to ridiculously slow speeds and then picking up and a fan that makes any creaking or high pitched squeals while running are signs that the fan is above to give up. If you can share a video of the fan in operation, especially the first scenario which can perhaps give us an idea as to the sinister nature of your little fan. 

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