The study subjected vehicles to simulated EMP attacks both while shut off and while running, and it found that none of the vehicles suffered any ill effects if the attack occurred while the engine was off. When the attack occurred while the vehicles were running, some of them shut off, while others suffered other effects like erroneously blinking dash lights.
Although some of the engines did die when subjected to an EMP, each of the passenger cars tested by the EMP Commission did start back up.
The study finding suggested that 90 percent of the cars on the road in 2004 would suffer no ill effects at all from an EMP, while 10 percent would either stall out or suffer some other ill effect that would require driver intervention. That number has no doubt gone up in the intervening decade since there are more cars on the road today that make use of delicate electronics, but none of the vehicles tested by the EMP commission suffered permanent damage.
The EMP Commission purposely backed off on the power of the EMP delivered to those vehicles because of bureaucratic imperative - they had to return the cars in working order. Royally phucking them up in a realistic, full power, test was not going to happen.