Cron stopped running; logs say: "Attempting to re-run cron while it is already running."
Summary

The error message you are seeing would happen if the following two conditions are met:


You cron jobs do not finish (error) or take more than 4 minutes to finish ;
You invoke cron more often than every 4 minutes (According to your crontab setting, not the setting in Drupal)


This error message is therefore a symptom of a cron tasks that is either failing or taking too long to run. (Note: I realise you have already found the culprit, but I wanted to add an answer for people who find this page via searches, as I did)

Background

The first thing to understand is how Drupal cron tasks are run. The Drupal cron is invoked at regular intervals - either through a cron job on your server, or after every page load if you use the poor man's cron which is Drupal's default.

The cron tasks are not necessarily run every time cron is invoked however - there is a setting in Drupal (default is 3 hours) which says how often cron tasks should be run. But this delay of 3 hours only applies if the cron tasks have finished successfully.

In Drupal 7, cron uses Drupal's locking mechanisms, which provides a cooperative, advisory lock system. One of the features of this lock system is that locks expire after a certain time. In the case of cron, it expires after 4 minutes - so if your cron is invoked every 3 minutes and the previous cron job hadn't finished by that time (either it crashed or was very slow), you would indeed get this error message.

The fact you set the cron to be every 12 hours does not make a difference - because the Drupal cron task is failing/taking too long, Drupal assumes it hasn't been run so tries to run it again as soon as cron is invoked. The twelve hour delay only applies to successful cron runs.

The cron semaphore variable does not exist any more in Drupal 7 - this was for an older version of Drupal. In Drupal 7 there is no reliable way to manually release a lock, because the locking backend might change - however if you are using the core locking mechanism then you can release cron locks by editing the database:

DELETE FROM semaphore WHERE name = 'cron';


But by doing this you would only be fixing the symptoms - the problem that needs addressing is why is cron failing / taking so long to run.