Change the setting in your MSDOS.SYS file:

Under [options]

AUTOSCAN=0

disable automatic scandisk.

AUTOSCAN=1

automatic scandisk, preceded by the error message (default)

AUTOSCAN=2

automatic scandisk with no error message.

You can also edit the scandisk.ini file in your \Windows\Command folder. When scandisk gets run automatically after an improper shutdown, it uses the /custom option which reads the settings from the scandisk.ini file. This file is well documented. Read through it to see how to customize scandisk.