Austin Weidner wrote:
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Does Net::DNS even look in resolv.conf? There seems to be some links to a
file called ".resolv.conf". I wonder if Net::DNS isn't even looking there?

According to the docs:

On UNIX systems the defaults are read from the following files, in the order indicated:

    /etc/resolv.conf
    $HOME/.resolv.conf
    ./.resolv.conf

What OS is this server running?

Try running this:

perl -MNet::DNS -e '$r=Net::DNS::Resolver->new;print join " ",$r->nameservers, "\n";'

You should get the same ip addresses that are in your /etc/resolv.conf

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