“There are issues with it. After some version somewhere in the 6.35..6.39 timeframe it stopped working because the script was started “too soon” after the boot and the router was not ready to accept the config commands. So it silently failed. This has not been fixed even today, but it can be remedied by putting a /delay 30 at the top of the file. (download it, edit it, and re-upload)”
from : http://forum.mikrotik.com/t/system-backup-containing-previous-version-of-edited-scripts/139015/10