A scan tool should not turn off you stability system. If your warning light was on, and there was any trouble codes associated with your system, then that tool may have erased the codes.
Look in your owner's manual for instructions on turning on/off your stability system. If you turn it on and any warning lights come on concerning that system, then there's a problem. A scanner will point you in the right direction.
And when this system malfunctions, it's almost always a sensor that has failed. Your stability system shares the same sensors with your ABS system, except the yaw sensor. So if it was a shared sensor, the your ABS light should also come on.