Well the boot-time scan after installation and reboot, before windows starts should only run once (unless you schedule it again). You can interrupt/stop it using the Esc key, but even switching off your flybook shouldn't have any impact and as far as I'm aware avast doesn't alter the MBR under any circumstances.
Have (or did) you another AV installed in this system, if so what was it and how did you get rid of it ?
This could cause conflict between the old and new and that conflict could have a symptom like this.