Likewise – still getting this. I have four WP control jobs, each a PHP script. One or two typically disappear every few days, having been running fine. If it helps to disagnose, the ones that disappear are those which are computationally heavier. The largest one takes perhaps a second to execute and is set to run every 5 minutes but still disappears. They are running on Amazon web services EC2 instance with load balancer etc, SQL hosted on AWS RDS service. Not sure if this is relevant but it might help track it down.
Me too. Had this about 3 times over last year. Love the plugin though!