You can't really resolve this unless you hae separate nameservers in ech TLD. Which would require you have a domain name for your nameservers in each TLD, and to set up nameservers for each.
This check made sense back when a second lookup cost more (in internet terminology), and when each domain was served on it's own IP# if not on it's own server.
Shared hosting made this check confusing, if not meaningless.
In other words, if you hosted the domains: example.net, example.com, and example.org, you'd set up nameservers at your registrar for example.net, example.com, and example.org. Until several years ago when the registrars started allowing multiple nameservers on the same IP# (yes, it's only been a few years) that meant separate IP#s for each nameserver, and in fact, that's the design that DirectAdmin follows by default (some TLDs may still require it, but we haven't run into it for several years now).
The way around it today is to set up (in your zone files) nsX records for each domain you host and A records for each nsX record, and to give your clients IP#s instead of nameserver names, and tell them to set up their own nameservers at their registrar.
We don't recommend the work around because of the customer support nightmare it creates. We live with the error (in certain reporting tools) and the extra lookup.
As does just about everyone else I know.
Jeff
