I think you need just one master zone, let’s call it example.com. So your website would be http://www.example.com/ .
And let’s suppose you have two nameservers, let’s call them ns1.test7878999.com and ns2.test7878999.com.
Make sure the domain registrar for example.com lists ns1.test7878999.com and ns2.test7878999.com as the name servers for example.com.
(Notice how the nameservers for example.com are not ns1.example.com and ns2.example.com? They could have been, but not in my example. If you keep the nameservers in a different domain, there is slightly less to go wrong. So long as test7878999.com itself is valid, you know people can find ns1.test7878999.com and ns2.test7878999.com. If the nameservers had been ns1.example.com and ns2.example.com, you would have run into a chicken-and-egg problem, because you can’t find ns1.example.com if you can’t find example.com, and vice versa. This is easily fixable, but you’re having a hard enough time making it work as it is, so I’m keeping things simpler by having your nameservers be outside example.com. Also, the reason I picked a long name like test7878999.com was to make sure it didn’t accidentally match a real domain.)
You might need to explicitly add NS records for each of your nameservers into each of your nameservers.
I.e., ns1.test7878999.com should have NS records listing both ns1.test7878999.com and ns2.test7878999.com as nameservers for example.com. And so should ns2.test7878999.com.
Basically, no matter whom you ask for a list of nameservers for example.com, you should get back the same answer. So whether you ask your domain registrar, or you ask ns1.test7878999.com, or you ask ns2.test7878999.com, they should all reply with roughly: “Name servers for example.com are ns1.test7878999.com and ns2.test7878999.com.” If anybody says anything different, then you might have problems.
Webmin’s DNS module should let make sure both ns1.test7878999.com and ns2.test7878999.com have NS records for example.com listing both ns1.test7878999.com and ns2.test7878999.com.
Or you can manually edit /etc/named.conf (or whatever the pathname for named.conf is on your machines).
But before doing so, I would wait a while, just to make sure it isn’t a lack of DNS propagation. And for good measure, you can restart named on all servers, so it has fresh data. (If you’re not sure how to restart named, rebooting the VPS will do it.)
And before or after that I suggest checking DNS for example.com at http://www.intodns.com/ and looking carefully at their diagnostics.