Hello,
My name is Dragos and I'm a Senior System Administrator with over 7 years of working experience for one of the top web hosting companies from USA - California. I have built and currently maintain a pair of 8 NS's, set up across different solutions: pDNS with MySQL and named (master <> master or master <> slave replications).
I will be more than happy to work on your project to get your DNS servers setup and to ensure that both of them are correctly answer to all the queries (those that are supposed to at least, based on their GLUE entries).
If you have any questions please let me know. If you can provide me the NS's pair and the IP address of each of them, I can have a preliminary investigation done, out of the box, in order to at least be able to tell the possible reasons of this behaviour.
Thank you,
Dragos