Configuring a nameserver

Since the last few days my sys-admin colleague (Sunil Mohan Ranta) and I have been working together to setup a nameserver for our institute. After about a complete evening of slogging (including the time we spent on installing Linux - Fedora Core 2, and learning about DNS's) we finally got it working by the evening. We are using named and configuring it was a breeze (not much to do actually). We had to configure it for the new domain www.iiit.ac.in that the institute is getting.

However, after some days now I find that when I compare the host query results of our newly setup nameserver with the ISP's nameserver we were originally using, the MX entries are missing. Actually, it's only the NS and A entries that figure out with our nameserver. I wonder whether it'd create problems if we use this nameserver for resolving on the mail-server. The nameservers obtained by the root nameservers for .net and .com actually give the same results (as the new NS), nevertheless. The best method, I guess, is hit-and-try. :-)