crazy problem with remote start and batt

Well I haver had a problem with my remote start where If I remote started my truck with my second battery hooked up my truck would shut off right away. If it isnt hooked up it runs just fine. I am wanting to hook up my battery isolater again but it dosent seem to work with my 200 amp alt.  Any ideas

do u have your remote starter in tachless/voltage sense mode or do u have the tach wire hooked up.?...I recall an installer at our company that had a problem close to yours.... i beleive he hooked his remote start  power direct to one of the batteries as his fix, i believe he said in tachless or voltage sense mode it seemed to work that way...im just relaying what i had heard.... hope it helps ..have fun