Its difficult to say without seeing the backend (Im not asking for access so dont think im a baddy :P)
Anyway, I can tell you im using the pretty perma links on my ec2 wordpress blog and it works fine?
see:
http://www.system-administration.net/step-by-step-tutorials/amazon-web-services-aws/create-new-ec2-instance/
Hopefully someone can help you out :S
