When you want to use our managed DNS hosting, you have to make changes to your domain’s name server settings. Changing name servers on Route53 isn’t quite as obvious as with other domain registrars. There are a number of instances where an NS record was created for a domain instead of changing the actual name servers for your whole domain which won’t work.
That said, on AWS Route53, you will need to follow the steps found in AWS’s DNS documentation.
Following these steps should get things working better. Let us know how it goes!