that depends on what the script is you are running....
it could be caught as a dead process if you don't have the correct path in the script and/or in the .profile for the user executing the cron command
root is running the script and it's root's crontab. I woudl epect since cron is always running that changes take right away but something keep running the script.
I'm puzzled! You are right in saying that if you edit the crontab script using crontab -e, comment out the appropriate lines and then save the changes, they should take effect immediately.
The same situation happened to me last year and I had to kill the process and reboot system. My cron job ran okay after the reboot. You might have a corrupted cron job or other process out there upsetting your jobs.
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