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I have problem with configuring bind9 on debian (lenny) server. Generaly speaking everything is working ok but sometimes I get 404 on few domains (eg. but after few refreshes in browser site loads) or I can't validate site with (error '500 Can't connect to (Bad hostname '')'). Domains were moved from other server. After moving I changed serial number in zone file.

$ttl 600
@       IN      SOA (

@       IN      NS
@       IN      A

www     IN      CNAME   @
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up vote 1 down vote accepted

It looks to me like a DNS caching problem, the upstream DNS server still knows about the old DNS and points towards there giving you the 404 problem.

Also the fact that it can't resolve sometimes is a bit dodgy, what I would do in your case is use the dig utility to check that all your new DNS servers are resolving the zone properly and with the same serial number

dig +search SOA DOMAINNAME
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The .com nameservers know nothing about; check with your domain registrar.

dig +norec +auth -t ns
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For addendum to what @mthenw wrote before, when bind9 is restarted, in /var/log/syslog there are such entries correspond to bind

Jan 17 16:49:24 r1688 named[30044]: network unreachable resolving '': 2001:500:49::1#53
Jan 17 16:49:25 r1688 named[30044]: network unreachable resolving '': 2001:503:231d::2:30#53

of course and are reached by ping;

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