You can try this, it has worked for me I found out by accident.
For an empty channel set the power % to 100 :
Assign the Fan channel to a curve controller just like you normally would, except set all the power settings at 0% on the controller. Use whatever temperature you want for a datasource.
For any other Fan header you are using set the header at 100%, then just use a controller.
In my experience anyway, the Fan channels are pretty well governed if a software controller is used.
If none of these work for you then something is going on I know nothing about.