Hopefully someone else can learn from this because the docs are a little deceiving, as you said it says in the docs that the order is checked like:
/etc/resolv.conf $HOME/.resolv.conf ./.resolv.conf
However it was checking like this: $HOME/.resolv.conf /etc/resolv.conf
I've submitted this information to the current maintainer of Net::DNS. Any changes I was making to /etc/resolv.conf were being ignored. Changes to $HOME/.resolv.conf were being accepted.
Actually, these files are essentially ANDed together. It doesn't just stop once it has read your /etc/resolv.conf, it keeps going and adds in servers from the other two files. The relevant code is here: http://search.cpan.org/src/CREIN/Net-DNS-0.48/lib/Net/DNS/Resolver/UNIX.pm
