Strangely enough, when I reboot my Ubuntu 12.04 server, the DNS no longer works, which makes the domain unavailable to access to my site. Normally the DNS should be working after a reboot, but this doesn't happen anymore. I use nginx to serve content, but nginx is already configured to work with my domains.

What are the typical practises must I do after a reboot and how can I solve this issue I experience? I already have BIND, networking and resolvconf to boot when the server boots up.

; <<>> DiG 9.8.1-P1 <<>> mysite.com
;; global options: +cmd
;; connection timed out; no servers could be reached

This is my output with dig

$ttl 38400
mysite.com.    IN    SOA    ns1.mysite.com. webmaster.mysite.com. (
            1055026205
            6H
            1H
            5D
            20M )
mysite.com.        IN    A     xx.xx.xx.xx # Server IP 
*.mysite.com.          IN    A     xx.xx.xx.xx # Server IP 
www.mysite.com.    IN    CNAME mysite.com.
ns1.mysite.com.    IN    A     xx.xx.xx.xx # Server 2nd IP
ns2.mysite.com.    IN    A     xx.xx.xx.xx # Server 3rd IP 
mysite.com.        IN    NS    ns1.mysite.com.
mysite.com.        IN    NS    ns2.mysite.com.
mail.mysite.com.   IN    MX    1 mysite.com.

This is the contents of /etc/resolv.conf

# Dynamic resolv.conf(5) file for glibc resolver(3) generated by resolvconf(8)
#     DO NOT EDIT THIS FILE BY HAND -- YOUR CHANGES WILL BE OVERWRITTEN
nameserver 85.17.150.123
nameserver 85.17.96.69
nameserver 62.212.64.122
search localdomain

After using more dig commands, outputs:

; <<>> DiG 9.7.3-P3 <<>> @85.17.150.123 mysite.com
; (1 server found)
;; global options: +cmd
;; Got answer:
;; ->>HEADER<<- opcode: QUERY, status: REFUSED, id: 24847
;; flags: qr rd; QUERY: 1, ANSWER: 0, AUTHORITY: 0, ADDITIONAL: 0
;; WARNING: recursion requested but not available

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

;; Query time: 2145 msec
;; SERVER: 85.17.150.123#53(85.17.150.123)
;; WHEN: Mon Nov  5 16:31:32 2012
;; MSG SIZE  rcvd: 30

; <<>> DiG 9.7.3-P3 <<>> @85.17.96.69 mysite.com
; (1 server found)
;; global options: +cmd
;; Got answer:
;; ->>HEADER<<- opcode: QUERY, status: REFUSED, id: 27879
;; flags: qr rd; QUERY: 1, ANSWER: 0, AUTHORITY: 0, ADDITIONAL: 0
;; WARNING: recursion requested but not available

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

;; Query time: 949 msec
;; SERVER: 85.17.96.69#53(85.17.96.69)
;; WHEN: Mon Nov  5 16:32:59 2012
;; MSG SIZE  rcvd: 30

; <<>> DiG 9.7.3-P3 <<>> @62.212.64.122 mysite.com
; (1 server found)
;; global options: +cmd
;; Got answer:
;; ->>HEADER<<- opcode: QUERY, status: REFUSED, id: 29293
;; flags: qr rd; QUERY: 1, ANSWER: 0, AUTHORITY: 0, ADDITIONAL: 0
;; WARNING: recursion requested but not available

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

;; Query time: 825 msec
;; SERVER: 62.212.64.122#53(62.212.64.122)
;; WHEN: Mon Nov  5 16:33:39 2012
;; MSG SIZE  rcvd: 30

With Google DNS (8.8.8.8):

; <<>> DiG 9.7.3-P3 <<>> @8.8.8.8 mysite.com
; (1 server found)
;; global options: +cmd
;; Got answer:
;; ->>HEADER<<- opcode: QUERY, status: SERVFAIL, id: 38498
;; flags: qr rd ra; QUERY: 1, ANSWER: 0, AUTHORITY: 0, ADDITIONAL: 0

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

;; Query time: 3982 msec
;; SERVER: 8.8.8.8#53(8.8.8.8)
;; WHEN: Mon Nov  5 16:37:27 2012
;; MSG SIZE  rcvd: 30