It's the way they're made to work on the 747 Classic. The one in question was a GE CF6-50 powered contraption, (with the reversed wiring being done at a certain Chinese maintenance company, not the company I flew for) and the reason it took so long is because they are really intended to be used in-flight, where the fuel-flow is far higher and so they will run out of fuel much faster than they would at idle. As mentioned in another post, other aeroplanes have slightly different systems, such as the 777 which has another shutoff valve closer to the engine so it shuts down much faster - the negative side of that is that the fuel line from the wing down to the engine still has fuel in it.
Quoting 18-Wheeler.
Just so we don't get confused with the initial airplane (737) the handle (on the 737) will only close the engine fuel shutoff valve. That's why the QRH tells you to shutdown the engine start lever first. If you wouldn't the engine would, indeed, continue to run for another 10 to 20 seconds because of the remainig fuel still present in the fuel system.