More often than I'd like I see issues where Drupal's cron fails or exceeds the time limit. Here is a handy Drush command which will run all cron hooks on your site and the time it takes to run. This will allow you to see which cron it fails on, and which ones run slowly. From there you can look at the hook_cron for that module and work out why it failed or why it is slow. The most common issue I see is related to search indexing and nodes that have php in with drupal_goto() or similar. Drupal tries to index the node, ends up following the goto, and forgets to continue with cron.

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