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Victory! It was definitely PEBKAC. I was putting in the DNS validation incorrectly into my DNS provider I kept entering it as

_acme-challenge.gateway.domain.tld=ValidationString

What I needed to do was add it under the *.gateway.domain.tld domain with the string. It made more sense to me when using CertifyTheWeb and the validation was coming back with

*._acme-challenge.gateway.domain.tld=ValidationString