Isso foi respondido pelo pessoal da AWS nesta postagem no fórum . Para a posteridade, aqui está a resposta da Cindy @ AWS:
Windows Server 2008 AMIs are only available for EBS-backed instances. It is not currently possible to save a Windows Server 2008 instance into an S3 AMI. In order to save your instance as an AMI, you should use either the EC2 API tools command ec2-create-image or (in the AWS Management Console) choose "Create Image":
http://docs.amazonwebservices.com/AWSEC2/latest/UserGuide/creating-an-ami-ebs.html