Hello,
I allow myself to continue this thread because my problem is similar and no solution is proposed.
I have WHMCS 7.4 and the registar module NETIM.FR (distributed separately) and although I defined the "Netim" registrar in the "Domain prices" page, when the domain is created by the order, it is set to empty.
I have to configure all domains manually. Activity log:
12/02/2018 12:22 - Modified Domain - Registrar changed from '' to 'netim' - User ID: 1 - Domain ID: 29
I read the documentation page on Auto Setup, and everything seems fine ... https://docs.whmcs.com/Auto_Setup_Issues