I am not sure if it will work for you or not, but here is what I did that got around the issue.
In the Add-on configuration of inputs,
-edit the CloudWatch input and then "Edit in advanced mode" and remove the AWS/S3 Namespace totally and save/update
-Create a new CloudWatch input (slightly different name) and delete all of the Namespaces except AWS/S3
--- in this new input for just AWS/S3 change the period value under "Advanced Settings" to 3600
The value for Period has to be the same for all of related Namespaces so you cannot change just this one without creating a new input, even in the inputs.conf file (it does not like any variation in period within the same defined input) and the S3 bucket CloudWatch metrics are only reported once per day, that may be the issue.
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