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The real root cause is that your server has a protection against the same IP accessing the same URL or script file repeatedly over a short period of time. Typically, this is implemented with an Apache module. On cPanel hosts that's mod_bwlimited. Some hosts may use different approaches but the effect is the same. Since this information is neither publicly available nor detectable in a way we work around this server protection by ensuring there is a minimum amount of time spent on each request during the backup. This is the minimum execution time.

Detecting the minimum execution time works by making three consecutive requests, each trio of requests made after setting the minimum execution time to different values: 0, 0.5 seconds, 2 seconds etc. If the first trio of requests gets blocked it's possible that the server denies further requests, making the detection fail. That's why it tells you to configure Akeeba Backup manually.

Use the Configuration page in Akeeba Backup to set minimum execution time 2 seconds, maximum execution time 7 seconds and execution time bias 75%. If this doesn't work try setting the minimum execution time to 5 seconds instead. Increasing the minimum execution time makes the backup slower but works around the server protection essentially killing off the backup process prematurely.

You're welcome!