Hi,
Searching the code for that error, it seems to happen if there is a "url" type resource which is not part of your site. The search indexing code is trying to look at the page linked, and prints a message to say it won't look outside the site.
Looking at the code, it looks like this is just a notification and wouldn't cause the cron to stop. Perhaps there is something else that's broken but no error is being shown.
Could you try turning on debugging - site admin > server > debugging > show all errors, and see if anything else comes up?
Simon