for some reason when I got my new alarm installed, the thermo fans turn on when IGN is ON and immobiliser is active, but when I press the fob button to disable the immobiliser (then start car), fans go off and work normally... weird.

My theory is, it could be the immobilizer not supplying power to the amp and other components. With no power to the amp means the fans run on full speed. Though I don't understand why it doesn't give power to the amp when you turn the immobilizer off (when the key is in IGN ON position). Maybe its the design of the alarm to not to complete the circuit or give power until the engine is running as an extra precaution?