Hi Mike,
Are you using S3 as the origin for your files for any particular reason? I had been but when this problem arose, I started using the generic mirror to have Amazon Cloudfront (Which incidentally is the real CDN... S3 is not a CDN. It is just storage.) pull the files directly from my server instance taking S3 out of the picture.
If that is an option for you, I would recommend trying to configure it that way so you don't have to deal with the S3 issue.
Here is a link to a tutorial that should help walk you through that process: https://rtcamp.com/tutorials/cdn/amazon-cloudfront-wordpress-w3-total-cache/
Hope that helps!
