Server 3 / SSL Certificate / Open Directory - Problem!

We've updated from Server 2 to Server 3 / OS X 10.9.
We have an SSL certificate for server from Comodo.
Under Server 2, all worked just fine, with the SSL certificate being used to secure all services (configure via Server app).
Under Server 3, all works just fine, but Open Directory will not accept certificate - so Certificates / Settings in Server 3 app shows "Custom Configuration" for Settings - and on inspecting this it is because Open Directory set to be not secured but everything else is using SSL.
I've tried setting the Open Directory to use the SSL, but when ever I do it simply bounces back to being unsecured.
Does this matter?  Presumably it should be possible (as the standard setting appears to try and set Open Directory to use the SSL certificate), but not sure whether trying to fix is simply a fools errand.
Anyone got any clues as to whether to fix or not, and if to fix, how?
Thanks in advance.

Have you check to see that the certificate is indeed "Trusted" by your server?
Above, you stated that they're in the etc/certificates folder, but that doesn't mean that the server likes them.  You can create a "Self Signed" Certificate and still have certificates in there.  That doesn't mean that anyone else on the planet has to trust them.
Open Keychain Access in your utilities folder.  Depending on how you have it configured, you may have to look around to find the certificate in question.  It may be under login, or System. 
When you select your Certificate, if it's there, does it show as trusted?
Another thing you can check...  Often times Certificate authories, use Intermdeiate certificates.  Since anyone can sell a certificate, in order to have it trusted, you need to have it signed by someone else.  A good example is Godaddy.  They sell both SSL and Code signing certificates of all flavours.  In order to get them to be trusted, the "Intermediate Certificate" needs to also be installed in the keychain.  My Godaddy cert looks to be trusted by Verisign via an intermediate.
Have a look here...  https://support.comodo.com/index.php?_m=knowledgebase&_a=viewarticle&kbarticleid =1182
Not sure if it's directly relevant, but there it is.
The point is, I think you need to verify that your certificate is trusted by your server.  OD won't use an untrusted certificate. 
--an afterthought--  Anything in the logs?
Open up your server window where you try to select the certificate for OD.  Also, in another window open up the terminal.  In terminal, type:
tail -f /var/log/system.log
In the server window try to select the certificate and click done.  See what the output in terminal says.

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    In my particular circumstance, I've now got ALL Leopard clients, one Leopard v10.5 server, and one Tiger v10.4 server. Everything is working fine now, but it was not a simple matter getting the Tiger v10.4 server re-integrated into the otherwise ALL Leopard environment. OD/Kerberos is on the Leopard v10.5 server. Home directories are still on the Tiger v10.4 server.
    Two keys to getting THIS/MY set-up working:
    1) Tiger v10.4 server needs to have Open Directory set to "Connected to a Directory System" and has to be joined to the Kerberos realm that was set-up on the Leopard v10.5 server (use Server Admin to do all of this).
    2) Sharepoint on Tiger v10.4 server has to have SOME, but NOT ALL checkboxes for guest access enables/checked. See:
    http://discussions.apple.com/message.jspa?messageID=10903468#10903468
    Number 2 immediately above is contrary to what Apple manual for User Management reads, but this is what worked for me/my set up, after pulling my hair out following the manual's instructions to the letter and not getting the thing to work!

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