Me parece que el problema que comentas es porque en la maquina que tienes corriendo bind9 como dns local lo tienes corriendo con dhcp:
/etc/network/interfaces
iface eth0 inet dhcp
es por ello que cuando reinicias el servicio de network obviamente te asignara una ip asi como tambien los dns de tu proveedor, entonces sugiero que pongas una ip estatica y de igual manera asignes estaticamente los dns en /etc/resolv.conf, entonces cuando reinicies el servicio de network veras que no se cambian los dns.
[quote]
Ya que como entiendo (por favor correjir), las peticiones DNS que le lleguen al server, serian consultadas localmente (127.0.0.1), y si no estan ahi, luegos se le solicitan al DSN del ISP, esto es c
Correcto?
[/quote]
Si es un Dns local me imagino que debes tener en los archivos de host (/var/named/xxxxx) los host que desees anunciar, y en el archivo de zona (/etc/resolv.conf) la opcion forwarders a los dns externos de tu isp, entonces cuando los clientes hacen peticiones de dns a tu server de dns local el busca si los tiene y te responde caso contrario la peticion es enviada a los servidores que estan publicados como forwarders.

Saludos,

DNS cache Local

# aptitude install bind9

Luego editamos
# vim /etc/bind/named.conf.options

options {
directory "/var/cache/bind";

// If there is a firewall between you and nameservers you want
// to talk to, you may need to fix the firewall to allow multiple
// ports to talk. See http://www.kb.cert.org/vuls/id/800113

// If your ISP provided one or more IP addresses for stable
// nameservers, you probably want to use them as forwarders.
// Uncomment the following block, and insert the addresses replacing
// the all-0's placeholder.

forwarders {
208.67.222.222; --> OpenDNS
208.67.220.220; --> OpenDNS
200.44.32.12; --> Cantv.net
200.11.248.12; --> Cantv.net

};

auth-nxdomain no; # conform to RFC1035
listen-on-v6 { any; };
};

Luego editamos:

# vim /etc/dhcp3/dhclient.conf

# Configuration file for /sbin/dhclient, which is included in Debian's
# dhcp3-client package.
#
# This is a sample configuration file for dhclient. See dhclient.conf's
# man page for more information about the syntax of this file
# and a more comprehensive list of the parameters understood by
# dhclient.
#
# Normally, if the DHCP server provides reasonable information and does
# not leave anything out (like the domain name, for example), then
# few changes must be made to this file, if any.
#

option rfc3442-classless-static-routes code 121 = array of unsigned integer 8;

#send host-name "andare.fugue.com";
#send dhcp-client-identifier 1:0:a0:24:ab:fb:9c;
#send dhcp-lease-time 3600;
#supersede domain-name "fugue.com home.vix.com";
#prepend domain-name-servers 127.0.0.1;
request subnet-mask, broadcast-address, time-offset, routers,
domain-name,domain-search, host-name,
netbios-name-servers, netbios-scope, interface-mtu,
rfc3442-classless-static-routes;

#domain-name-servers --> este estaba despues de domain-name,

#require subnet-mask, domain-name-servers;
#timeout 60;
#retry 60;
#reboot 10;
#select-timeout 5;
#initial-interval 2;
#script "/etc/dhcp3/dhclient-script";
#media "-link0 -link1 -link2", "link0 link1";
#reject 192.33.137.209;

#alias {
# interface "eth0";
# fixed-address 192.5.5.213;
# option subnet-mask 255.255.255.255;
#}

Luego editamos:
# vim /etc/resolv.conf
# resolv.conf created by pppconfig for movilnet

nameserver 127.0.0.1

Listo, podemos hacer una prueba de tiempos con: dig
$ dig bbc.com

; <<>> DiG 9.5.1-P1 <<>> bbc.com
;; global options: printcmd
;; Got answer:
;; ->>HEADER<<- opcode: QUERY, status: NOERROR, id: 27914
;; flags: qr rd ra; QUERY: 1, ANSWER: 1, AUTHORITY: 2, ADDITIONAL: 1

;; QUESTION SECTION:
;bbc.com. IN A

;; ANSWER SECTION:
bbc.com. 360 IN A 212.58.251.197

;; AUTHORITY SECTION:
bbc.com. 172800 IN NS ns0.thny.bbc.co.uk.
bbc.com. 172800 IN NS ns0.thdo.bbc.co.uk.

;; ADDITIONAL SECTION:
ns0.thdo.bbc.co.uk. 85322 IN A 212.58.224.20

;; Query time: 1358 msec <---------- Tiempo --------------->
;; SERVER: 127.0.0.1#53(127.0.0.1)
;; WHEN: Sun Apr 19 01:05:38 2009
;; MSG SIZE rcvd: 112

Lo hacemos de nuevo:

$ dig bbc.com

; <<>> DiG 9.5.1-P1 <<>> bbc.com
;; global options: printcmd
;; Got answer:
;; ->>HEADER<<- opcode: QUERY, status: NOERROR, id: 38252
;; flags: qr rd ra; QUERY: 1, ANSWER: 1, AUTHORITY: 2, ADDITIONAL: 2

;; QUESTION SECTION:
;bbc.com. IN A

;; ANSWER SECTION:
bbc.com. 304 IN A 212.58.251.197

;; AUTHORITY SECTION:
bbc.com. 172744 IN NS ns0.thny.bbc.co.uk.
bbc.com. 172744 IN NS ns0.thdo.bbc.co.uk.

;; ADDITIONAL SECTION:
ns0.thdo.bbc.co.uk. 85266 IN A 212.58.224.20
ns0.thny.bbc.co.uk. 86344 IN A 212.58.227.47

;; Query time: 1 msec <---- Nuevo tiempo ---->
;; SERVER: 127.0.0.1#53(127.0.0.1)
;; WHEN: Sun Apr 19 01:06:34 2009
;; MSG SIZE rcvd: 128

Dicen que el tiempo es dinero, lol

Estos lo tengo configurado con Debian Lenny

Saludos
Ft.