Ensure you have "enable user defined software automatic fan control" checked, in the FAN tab of "Settings". I have my fan bar-graph customized in this tab, btw. In the main AB window, I have Fan Speed "auto" ON and idle sitting at 40%, as I like my GPU fans on constant.
When I set this up, I hit "apply", then hit "save", the hit profile "1" (as it's the only profile I have) and clicked on "apply oc at system startup" and that's it.
This will allow my custom fan setting to run at windows start without having to do anything else, as AB will load when windows boots...