If your second nameserver is on the same server as your primary one, don't worry because just one nameserver is enough, however this is very strange because most registrars have to verify the existing of nameservers before add them to database. Try to contact the registrar again maybe they have answer for you.
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But yes, both DNSs are actually hosted on the same machine, and theoritically, I don't see a problem. The registrar did verify the 2 nameservers (I had to key in their ip addresses before it would allow me to add the, and they had to match).
I think it's a very strange occurance really, which in theory shouldn't affect anything... I just wasn't sure if that would be so.
I was actually thinking the exact same thing - recommend my customer move to a different registrar (probably namecheap since I use them too) - this really stems from the registrar not responding to emails. (I had sent the parent 1 email but no response from them either...)