Depending on the answer to these questions:
Is this Server behind NAT?
Is this the only server on your private Network?
If not is there another Server that is providing local/private DNS resolution?
If there is has appropriate DNS Records been created on that Server for your Mac Server?
Then this statement:
" . . . this is NOT a DNS . . . server . . . just a lowtech fileserver"
is probably the root of your problem? In which case an answer to your questions "Is there a concern? A bug? A misconfiguration?" is probably misconfiguration arising from (with respect) ignorance on your part.
If this is the only server on your network and it's behind NAT then you must configure DNS Services on the Mac Server just for stability reasons alone. No-one else need use this DNS Service just as long as the Mac Server itself uses it is all that matters.
You are aiming to low. Although these Apple Forums have questions from some of the most technically ignorant people I have ever read, you assume I'm there! I should have stated I've been working on Windows Servers for 15 years.
I figured that if I mentioned that it's NOT a DNS/DHCP server that most likly infers that I know what those services are and do and they are not doing the work on the offending server...and that they are running somewhere else, which they are (on a Win 2008 R2 server)...and the Mac is in the DNS records.
Forgive me as no offence was intended. If you had stated earlier that DNS Services were elsewhere and appropriate records created I would not have responded. There have been many posts from those who have heralded their understanding of DNS etc only to find out later on the problem was with DNS all along. Now I'm not saying that is true for you but as you can appreciate none of us can assume anything as usually - as you know - doing so makes an arse . . . .
As for it being a bug I'm not really sure although I would say . . . probably?
I have seen this problem before and it's sometimes associated with dual NICs however not always. If you launch Terminal and issue this command:
sudo scutil --set HostName server.pretendco.com
and monitor the situation afterwards it may hopefully fix the problem? Out of interest whas is the fqdn of your server anyway?
There are a couple? several? threads about this. I only found this one.
I've never been able to fix it. And I can't find the thread where someone had the explanation for it. If (big if) I recall correctly it has to do with how Mountain Lion handles hostnames dynamically.
Again, if I recall how this works, at boot, the system first grabs and set the .local hostname -- which is usually set in the Sharing System Preference. But because we're all using Server and not just client, the server hostname setting (FQDN) kick in, and our Servers switch from the .local to whatever our fully qualified domain names are. I remember looking at the Console logs -- to see what's happening at boot -- and configd is setting the hostname on my server to the FQDN, even if I've never changed it.
It's pretty much a nuisance which I just ignore, and thankfully I don't see much since I leave my Server on all the time.