All that happens in the ECM, as far as fan on with jakes. Very unlikely to be a problem w/ ECM as there isn't any opposite setting. Not sure where the fan solenoid is on an ISX, but what you need to do is trace back the harnesses from the jakes and the fan until they meet up, your trouble is most likely between that junction and the ECM. Like @mndriver said, check the grounds and for open wires in the harness (usually where the harness is bent around the engine, cab, or frame.)By always do you mean it never shuts off, are you running your AC?
The default for those is if there is a problem to turn on.
@Hammer166 might know of a related problem taking out the jakes. I know the fan automatically kicks on when the jakes engage when set to factory settings but this is the opposite so?