Problems with local DNS after 10.6.8

Question

Have a Snow Leopard server that's been running quite well. After (I think) the 10.6.8 update, I've encountered a really weird error regarding dns - the internal DNS doesn't recognize the top level DNS domain (companyname.net), so internally we can't see the site. Externally though, it's fine. Additionally, after about an hour or so, the local DNS entries seem to just stop working and it *seems* to crash, even though Open Directory still works fine, as do the external mail ips and website.
My DNS/web aliases have been working great for years now and are set up as the following.
10.6.8 Server: macpro.companyname.net
DNS zone: companyname.net
companyname.net alias to macpro.companyname.net.
www alias to macpro.companyname.net.
Web Admin is set up as the following:
Hostname: companyname.net
Web server aliases: companyname.net, www.companyname.net
Everything had been working fine until the 10.6.8 update. The website would redirect both companyname.net and www.companyname.net to companyname.net. Users on the local LAN see the local IP, externally see the external public IP.
But now, it's as if the DNS record for companyname.net LOCALLY doesn't exist. I can't ping it at all from local machines. I'm not sure what the deal is, and I also can't figure out where the look in the logs for assistance. I see entries that say so there's some sort of rebooting going on, but I'm again, not sure why. Any help would be great appreciated! I've restarted, done tons of cache reloads, deleted and readded entries - but as of now, still nothing.
27-Jul-2011 13:56:44.265 received control channel command 'freeze'
27-Jul-2011 13:56:44.282 freezing all zones: success
27-Jul-2011 13:56:44.360 received control channel command 'reload'
27-Jul-2011 13:56:44.360 loading configuration from '/private/etc/named.conf'
27-Jul-2011 13:56:44.360 using default UDP/IPv4 port range: [49152, 65535]
27-Jul-2011 13:56:44.360 using default UDP/IPv6 port range: [49152, 65535]
27-Jul-2011 13:56:44.390 reloading configuration succeeded
27-Jul-2011 13:56:44.390 reloading zones succeeded
27-Jul-2011 13:56:44.390 zone 1.0.10.in-addr.arpa/IN/com.apple.ServerAdmin.DNS.public: loaded serial 2011072701
27-Jul-2011 13:56:44.390 zone companyname.net/IN/com.apple.ServerAdmin.DNS.public: loaded serial 2011072710
27-Jul-2011 13:56:44.394 received control channel command 'thaw'
27-Jul-2011 13:56:44.395 thawing all zones: success
27-Jul-2011 13:56:44.395 zone 1.0.10.in-addr.arpa/IN/com.apple.ServerAdmin.DNS.public: loaded serial 2011072701
27-Jul-2011 13:56:44.395 zone companyname.net/IN/com.apple.ServerAdmin.DNS.public: loaded serial 2011072710
27-Jul-2011 14:10:30.754 received SIGHUP signal to reload zones
27-Jul-2011 14:10:30.754 loading configuration from '/private/etc/named.conf'
27-Jul-2011 14:10:30.755 using default UDP/IPv4 port range: [49152, 65535]
27-Jul-2011 14:10:30.755 using default UDP/IPv6 port range: [49152, 65535]
27-Jul-2011 14:10:30.756 no longer listening on 192.168.233.1#53
27-Jul-2011 14:10:30.885 reloading configuration succeeded
27-Jul-2011 14:10:30.885 reloading zones succeeded

Answer 1

Here's the zone file.
$TTL 10800
example.net. IN SOA macpro.example.net. canderson.example.net (
           2011072714          ;Serial
           20864                    ;Refresh
           3600                    ;Retry
           14976                    ;Expire
           345600                    ;Negative caching TTL
example.net. IN  NS macpro.example.net.
macpro IN  A 10.0.1.2
ichat IN  CNAME macpro.example.net.
www IN  CNAME macpro.example.net.
wiki IN  CNAME macpro.example.net.
mail IN  CNAME macpro.example.net.
ftp IN  CNAME macpro.example.net.
example.net IN  CNAME macpro.example.net.
I have been using mostly dig, nslookup, and ping to diagnose the problem. nslookup returns identically on the server and all clients, saying:
nslookup example.net
Server:                    10.0.1.2
Address:          10.0.1.2#53
*** Can't find example.net: No answer
"dig" also returns the same on the server and all clients, but this time actually finds something.
dig example.net
; <<>> DiG 9.6.0-APPLE-P2 <<>> example.net
;; global options: +cmd
;; Got answer:
;; ->>HEADER<<- opcode: QUERY, status: NOERROR, id: 39203
;; flags: qr aa rd ra; QUERY: 1, ANSWER: 0, AUTHORITY: 1, ADDITIONAL: 0
;; QUESTION SECTION:
;example.net. IN A
;; AUTHORITY SECTION:
example.net. 10800 IN SOA macpro.example.net. canderson.example.net.example.net. 2011072714 20864 3600 14976 345600
;; Query time: 0 msec
;; SERVER: 10.0.1.2#53(10.0.1.2)
;; WHEN: Wed Jul 27 16:24:55 2011
;; MSG SIZE  rcvd: 104
Lastly, I've been pinging the heck out of example.net. I've found that the server itself and Snow Leopard clients ping the correct internal address, but Lion clients (and iOS devices, oddly enough) return that it can't find the host.