System Status checks indicate that there was a hardware failure on the host that your instance was running on (AWS end). Stop starting the instance moves it away from the faulty hardware to a healthy host, basically each stop starts moves the instance to a different host. EC2 now has an automated service that does this and it had already triggered a stop start when you were rebooting on the console, and the stop start is what actually migrated the instance to a healthy host.
You can read more about System status checks below: https://docs.aws.amazon.com/AWSEC2/latest/UserGuide/monitoring-system-instance-status-check.html#types-of-instance-status-checks
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