IT is one of 2 things. The auto starters will shut the engine off after about a 15 minute run time automatically. This is done by the computer of the starter, that may be going bad. Also it has a anti theft feature, when you touch the brake pedal the engine will dye. so no one can steal it. I would start by looking into the brake switch. Is it adjusted properly? hope this will help some, Good Luck!
