Honestly, I'm not a DNS pro, but I added more nameservers in our registrar to point to R53 nameservers, then setup R53 to point to our Heroku app w/ alias support by following this guide: https://devcenter.heroku.com/articles/route-53
Are you using route53 to do an alias AND have the root domain use SSL? The setup at route53 is confounding me. I thought I'd setup a CNAME www.domain.com that points to sub.herokussl.com, and than an A record Alias that points domain.com to www.domain.com. But Amazon seems to not avow that the CNAME record is a "Record Set" that I can use for this.
Amazon doesn't like that Alias either. A friend on mine, Scott, just figured out though that you can point your Alias record at any ELB even outside your account: