DNS, Certificates, and Active Directory - School Setup Issues

Question

Our school has been piloting a small iPad depolyment.  I have been struggling with getting Profile Manager to work correctly since August of last year. Here's the setup:
1. Active Directory DNS/DHCP server (set as "school.local"--yes, I know .local is bad form, but it was set before I got here). I have changed the "Digest" to "Basic" setting
2. Mac Mini server that has its own external IP and hostname ("mac.school.org") and is also bound to the AD server for user authentication for services (Profile Manager, WebDAV, wiki, etc.). I have a self-signed SSL certificate installed under the name "mac.school.org"
3. About 90 iPads, and a handfull of Mac desktops
In a perfect world, users would be able to login (with their AD credentials) to the Profile Manager self-service portal using the external hostname of the mac server ("mac.school.org/mydevices"), install the Trust Profile, and enroll the device (iPad, Mac, etc).
However, this is not the case.  The setup seems to work for awhile; quite perfectly in fact. But then for reasons unknown to me, everything just "breaks" and Profile Manager ceases to work like it should. Here are some of issues I am seeing:
a.) DNS service on the Mac server turns itself ON randomly.  DNS should NOT be running this server, correct? All DNS lookups internally are done by the AD server. I've used changeip and everything matches (both say "mac.school.org")
b.) Whenever we use VPN, and at other seemingly random times, the server's hostname changes from "mac.school.org" to "mac.school.local" I would make the server external only, but it needs to have an internal IP to talk to the AD server.
c.) AD binding breaks randomly and I have to rebind the server to AD
d.) When enrolling devices, Profile Manager starts rejecting certificates (not a trusted source, etc.) and I have to destroy OD and PM and start all over again.
I know this is a lot and I'm not necessarily expecting anyone to answer all of these questions. I guess I'm wondering if anyone could point me in the right direction? I've looked for help with these issues all over the place, but none of the environments I read about are quite like the one I'm in.

Answer 1

Yes, I am not giving the real domain name here.
No prob. just checking, sometimes people have weird domain names never know if they are real or they expect them to be real or they put domain names owned by someone else on their internal network eek.
Not really needed to use mac.school.org internally, that is in local LAN. The thing to understand about DNS is the scope for which a DNS zone is relevant WRT a client machine — inside LAN or on Internet, and which DNS server is authoritative for a domain. Authoritative in the sense of 'the final word'.
Go to Network Utility on your mac, type in your real domain name (whatever you are changing to school.org to hide it) what comes back. On my server I see the below (I have replaced my real, Internet legal domain, to 'example.com')
In my setup I have, on the LAN, setup the Mac server to be authoritative for domain 'example.com'. On the Internet however it is another external DNS server.
So you have set DNS forwarders on the Mac machine?
I really don't believe that the machine's hostname is changing, it is statically configured. What I believe is happening is that DNS name resolution is telling you different things at different times because you are using different DNS servers.
On mac machine terminal type $less /etc/resolv.conf and copy paste what it says. In server app Services | DNS right side does it say you have forwarders?
Still it is not good to have two DNS domains in your internal LAN, there is no need to have school.org on the mac DNS unless it is going to be fully setup to be authoritative in the internal LAN for the domain school.org. You can have school.org on the Internet (Internet scope of users point 1) and school.local on internal machine (LAN scope of users).
Lookup has started…
Trying "example.com"
;; ->>HEADER<<- opcode: QUERY, status: NOERROR, id: 53292
;; flags: qr aa rd ra; QUERY: 1, ANSWER: 4, AUTHORITY: 0, ADDITIONAL: 1
;; QUESTION SECTION:
;example.com.                   IN        ANY
;; ANSWER SECTION:
example.com.     10800          IN        SOA          example.com. admin.example.com. 2013010907 3600 900 1209600 86400
example.com.     10800          IN         NS          server.example.com.
example.com.     10800          IN         MX          10 server.example.com.
;; ADDITIONAL SECTION:
server.example.com. 10800       IN          A          192.168.1.20
Received 145 bytes from 127.0.0.1#53 in 2 ms