Undefined index errors when running cron.php
You shouldn't run cron.php throught php cli. basically you should have a line like this in your crontab file:

0 * * * * wget -O - -q -t 1 http://www.example.com/cron.php

but you also need to append security token to the url.

by reading Configuring cron jobs using the cron command page you will get a better idea of how it works.