DNS Server Having Intermittent Issues with Open Directory

I work for a school and we're undertaking the large task of moving from Xserves running 10.6.8 to Mac Minis running 10.9. I have a lot of experience with OS X Server (I held ACSA up until they ditched it, and ACTC through the current OS) but I've hit a fairly large snag in configuring our DNS server. We currently run DNS via an AD server that is being retired at the end of the summer, so this is the first time our DNS will be Mac-based. That said, our network is ridiculously simple as we are a very small school. For the most part it's a flat network using the same IP range for our wired and wireless internal clients (we do have a vlan for guests but that's through Aerohive). I configured the DNS by hand, recreating the entries in our AD server (there were only about a dozen) and then adding in things that should have been there in the first place (e.g. printers and some other devices with static IPs that I'd like FQDNs for). Everything seemed to be working fine...until trying to log into Open Directory accounts.
For some background, the DNS server running 10.9 was the first server we upgraded and it was a completely clean install. We run DHCP on another Mac Server currently running 10.6.8 and it does have the proper OD server listed. All DNS entries for the OD server match our current DNS server. The issue is that it's taking some users 5-6 tries to log in with their network accounts. The errors they receive range from the login window shaking to it stating the user cannot log in at this time. This seems to be worse on client machines running 10.9. but it's appearing on machines running 10.6.8-10.9.3.
In my troubleshooting, I found that if I log in as a local user to one of those machines and do a dig for the OD server the results vary, this is where it gets weird. For example, if I dig ourodserver.ourdomain.org it will sometimes return host not found or it will sometimes resolve. If I ping the same thing it will sometimes work (even after stating it cannot resolve the host) and it will sometimes fail. If I then try a dig for the .local (e.g. ourodserver.local) it also yields the same varied results. However, on every machine that I've tested if I then open a Finder window and navigate to the server via the "Shared" menu and connect I have no trouble connecting and then magically my digs and pings in terminal work. If I revert DNS back to point to our old Windows server the issue goes away. I have meticulously combed through that server many many times now and am not seeing any missed entries. Any idea what could be causing this?

You must have a working DNS service, and the server's hostname must match its fully-qualified domain name. To confirm, select the server by name in the sidebar of the Server application window, then select the Overview tab. Click the Edit button on the Host Name line. On the Accessing your Server sheet, Domain Name should be selected. Change the Host Name, if necessary. The server must have at least a three-level name (e.g. "server.yourdomain.com"), and the name must not be in the ".local" top-level domain, which is reserved for Bonjour.
The primary DNS server used by the server must be 127.0.0.1 (that is, itself) unless you're using another server for internal DNS. The only DNS server set on the clients should be the internal one, which they should get from DHCP if applicable.

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