Yeah, this little monster can really keep you up at night.
Located in System > Configuration > Advanced > System > Cron (Scheduled Tasks)
These settings are very critical to making sure all scheduled tasks fire correctly.
What tends to throw your Magento store into a crazy ball of fire breathing bloated monkeys is when already scheduled tasks pile on top of already scheduled tasks and those scheduled tasks collide with other scheduled tasks and before long there is just not enough time in the day to complete the scheduled tasks before the other scheduled tasks get going and then bad things happen. Tasks stop getting executed and features stop working correctly.
3rd party extensions that have “special” cron schedules may need to be fine tuned to fit in nicely with what your Magento store is already doing in the Cron world.
One big issue that we have seen a lot is the Google Sitemap auto generation failing. What seems to fix this issue is to make sure your Cron settings for both native Magento extensions and 3rd party extensions are playing nice together. There really is not one set setting that will work for everyone. But there is a really nice extension that helps you monitor your cron schedules. You can find it here.
For example, we have a site that needs cron to fire every 3 minutes. This is due to a 3rd party extension that has some special time sensitive capabilities. We ended up tweaking Magento‘s System Cron to schedule tasks more tailored to the sites specs and usage times. Before we did this, the Magento store was using the default settings causing the 3rd party extension’s tasks to pile up and create bottlenecks.