I have the box's DNS nameserver hardcoded in /etc/network/interfaces with
(I just have to google DNS during testing, using another DNS live.)
And then I have dnsmasq running on the box to be a DNS cache, but also to rewrite a few DNS entries to point to Apache as a proxy.
Now for some reason I haven't been able to figure out the box is using dnsmasq for it's DNS server whenever dnsmasq is running, despite what the DNS nameserver is set too. If I have dnsmasq set to to listen on all interfaces and 127.0.0.1, all lookups just go through dnsmasq including the ones that are supposed to be proxied so it just gets caught in a loop instead of proxied. If I use don't use lo and comment out listening on 127.0.0.1, I don't get DNS at all.
There is no iptables rule or anything redirecting all DNS traffic, only allowing access only to our IP range.
There must be something that I am missing, but I can't figure it out.
With dnsmasq disabled digs go through the set DNS, with it enabled it goes through 127.0.0.1