If you are referring to the initial long boot-time scan before windows boots, you needn't worry as this is a one shot deal, it happens if you allow it after installation. It doesn't happen on boots after that unless you schedule it and then again it only applies for the next boot only.
If this is what you mean then this is how you can select it if required.
If you have XP, vista32bit or Win2k, you could enable a boot time scan. Right click the avast icon, select Start avast! Antivirus, a memory scan will take place followed by the opening of the Simple User Interface, Menu, 'Schedule boot-time scan...' Or see
http://www.digitalred.com/avast-boot-time.php.