Under Yosemite 10.10.x same issue or so it seams. Certificate from GoDaddy would apply easily to all services except Open Directory (OD). Thought nothing of it, server seemed to be running OK. OD service insisted on keeping one of the self signed certs. Not really though as I later found that I could neither create new network users nor change user's passwords and only got the error:
"existing connection is not authenticated or secure: password change denied"
Went through gytrations of turning off OD, selecting the GoDaddy cert, watching the Certificates interface revert back to the built in cert, Server app crashing, eventually OD selected "none" on its own. It eventually let me select the GoDaddy cert with OD off. Turned OD back on, it stayed. Then a little while later, OD reverted back.
Finally I reverted to the "servername..ocal - server name.local OD Intermediate CA" on everything. No use. Cannot change passwords, create users, set password policy. In fact, another bug because "Edit password policy" just fails to confirm, no error message, nothing. OK, OK, OK, give up, Cancel.
<rant mode>This is the kind of disconnect that happens when a bucket of command line tools are integrated using a GUI app, instead of developing a robust fully integrated app. iTunes is a great example of robust operations when a product is not a bucket of command line tools held together by baling wire and bubble gum. If iTunes failed like this, Microsoft would be running the music industry. Case in point, with these repeated fails of Apple server products, Microsoft is running the server industry... </rant mode>