Hi maier2505,
With the search function and "fancontrol" you should already find here in the BM2LTS area where to find the right threads to make fancontrol work.
Nothing on fancontrol is in search except my post. Please show me where that post is ?
But please tell me why you are connecting the fan to the Kontron Board ?
I am trying to reduce the noise of the main fan. It was also useful to know the rpm of the fan and the loud noise is equal to 1400 rpm.
Therefore, searching for a way to reduce the rpm and in doing so reduce noise without compromising performance.
This led me to try different fan connections on the Kontron board but also on the small power board next to the psu.
The connection to the small power board seemed as though the fan was making less noise but on the Kontron board made slightly more. However, on installing an app from Ubuntu called psensor, you have temperature and rpm readings .
Fan 1 , had a value of 1400 rpm which was the Kontron main cpu fan.
On placing the fan connector on the small power board there was no reading. It made sense to me to know the rpm so i could lower the reading.
The only set back is how to do this and so i googled and found fancontrol . Following the method of a post , i tried to modify the reading but our BM2LTS image is not the same as an ordinary Ubuntu , so this ended in failure, hence, this post.
Originally it is connected to the small Power board...
Yes, i know , thanks. 
I have a spare fan and so yesterday on changing the fan registered 1000 rpm. This is acceptable, the fan makes some noise but it is ok.
Thanks for helping.