I just did an upgrade from FreeBSD 5.3 to FreeBSD 6.1 on one of the machines here which happens to be my secondary DNS server. Lo and behold, BIND stopped working (it had been upgraded to 9.3.2). Well, it's not the first time that an upgrade introduced configuration issues that didn't used to be there previously.
I found these tips useful to get things back in order: Permission Denied error on secondary DNS server (from revsys.com). I also used the opportunity to tighten up security some more, it's always a good idea to do that anyway while I'm in there digging around.
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