Use the USB program to make sure that all of the settings on the 2140 are the way you think they are. Especially ones associated with shutdown.
Also, it sounds like your 2140 is in exact opposite sync with the car. In other words, it is executing the shutdown sequence when you start your car and the startup sequence when you shut the car off.
Try completely disconnecting the 2140 from all power for at least one minute, then plug everything back in and see if it works properly.