At ignition on then turned off. Will not stop running? Electrical which module?

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Occured on May 15 2010 15 miles of Charlotte, NC. Accourred again that evening, dead battery. Purchased new one at the failure at May 13. Tow home, 110 miles. Local garage said cd has to be restore to clear computer. Seems ...disconnect the 3 connections it would reset itself? Is that right? They want $89 to diagnose, and $100 more to fix. Is that reasonable? notify tom.neighbors@gmail.com