Alternator Question

Ok so I just finished wireing up my dual batt system and have an isolator for the charging. wire goes from the alt to the alt terminal of the iso and the stater batt goes to the main terminal and the acc batt goes to the aux terminal. Start up the Jeep and the alt is not charging pull off the alt wire from the iso and hook it up direct to the batt start the Jeep and it works fine. Put it back on the iso, start and nothing. Jump the main terminal to the alt terminal start the Jeep and it charging diconect the jumper and it continues charging through the iso like its supposed to. So any ideas on how to get the alt to start on its own. Do I have to give a signal to one of the two wires from the conector on the alt, if so which on? Or do you think the iso if faulty and I should get another one?
TIA Fletch