Hi @blaker elasticsearch is on a different host and this issue was occuring across all of the fleet hosts with the agent policy.
The issue is (and please check this out) that in the official agent download archive system.yml is not system.yml.disabled in the nested metricbeat archive.
This may be for users manually downloading the agent...?
When I had the issue with the new host, I removed the API keys and reset the fleet policy for the rest of the hosts with this policy even though the issue didn't apply to all of them. I then removed and re-installed a fresh elastic agent on all hosts (using the link in the post above). This now meant that all hosts exhibited the same issue until I renamed system.yml back to its disabled form as @Michal_Pristas found.
TLDR; The current elastic agent (Windows at least and re-downloaded just now) for download from: Download Elastic Agent Free is the problem: elastic-agent-7.14.1-windows-x86_64.zip\elastic-agent-7.14.1-windows-x86_64\data\elastic-agent-703d58\downloads\metricbeat-7.14.1-windows-x86_64.zip\metricbeat-7.14.1-windows-x86_64\modules.d\system.yml needs to be renamed to system.yml.disabled
I could be wrong with the above evaluation, however this has resolved the issue for me on 8 hosts.
Thanks again for all of your help @Michal_Pristas, @blaker, @ruflin