This same problem was happening to me only when I used a CDN. I set the options to ignore that file from being called from the CDN and now it works perfectly. Guessing because this file needs to be written to, the permissions to this file need to be set to writable but for some reason when hosted on S3 with full permissions it wont work.

So a quick fix, just set that file to be ignored by the CDN and it will be called normally from your web server. On W3 Total Cache its the Reject files option under the CDN section. Hope that helps.