I doubt very much that it would be anything to do with having two dots in the domain name. Think of all the companies out there that have two part TLD’s such as “.co.uk” for example, or blue chip companies such as Novartis that have the division in the email domain, e.g. “pharma.novartis.com”.
My question would be is the domain part of the address being given by the AS400 a valid domain. If it’s not then it could be that Lotus Notes is rejecting it as spam.
Hope it helps