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You should not call/run cron.php directly but cron.sh via system cronjob/crontab instead.

I can recommend Fabrizios Blogpost for more information about the Magento cron:

cron.php vs. cron.sh

In Magento’s root folder there’s a cron.php file and a cron.sh file. Briefly explained cron.sh internally calls cron.php and takes care of not executing more than one process in parallel. That’s a good thing, right? Well, sometimes… If you have long running tasks (e.g. a product import implemented as a task), these tasks will prevent anything else from being executed until the task has finished. You might have some other important tasks that shouldn’t wait or be skipped just because another task is running. Check the “Missed if Not Run Within” setting to configure the maximum delay a task can have to still be executed.

On the other hand using cron.php will start a new process every time it’s being called which could easily result in performance problems or race conditions for tasks operating on the same data. This is why cron.php should not be called directly. Find out more about cron groups later in this blog post for a nice solution on how to handle this situation.

http://www.webguys.de/magento/tuerchen-08-magento-cron-demystified/

First off, Magento's default cron handling is (nicely put) a little strange. Please have a look at the Aoe_Scheduler (https://github.com/AOEpeople/Aoe_Scheduler), which provides a very convenient user interface and helps you find possible errors in your setup more easily. In addition, it comes with a custom shell script that you can extend to your needs.

I mention the Aoe_Scheduler as it handles potential deadlocks that might occur in vanilla Magento cron setup better. We've experienced deadlocks with cron jobs in Magento in the past for commands that might exceed defined timeouts. Aoe_Scheduler fixed these issues.