Mingyar,
I am not sure whether I understand everything you are saying, and I am not a linux user. So chances are that I misunderstand the situation.
autorun.sh is run before rcS, right? At the point, when you call
Code:
echo "autorun" >/mnt/onboard/.kobo/autorun.log"
mnt/onboard is not yet mounted, therefore you cannot write to /mnt/onboard/.kobo/autorun.log.