Why was my GoDaddy SSL Cert "Not from a Recognized Authority"

I've seen many reports here of people experiencing problems installing and renewing SS Certificates in OS X Server.
In my case a simple Certificate renewal turned into a Very Worrying Episode as the new certificate was "Not from a recognised authority" according to OS X Server 3.1.2 on Mavericks. Email clients could not log in etc. etc. without being told the server was insecure.
I tried several times to renew the certificate. Last year's was from GoDaddy and we had no problems. This year was not straightforward and has wasted 8 or so hours of my life.
This is of course only anecdotal, but it seems that OS X Server cannot properly install SSL Certificated generated from SHA-2 but can from SHA-1. SHA-2 is the default at GoDaddy now (SHA-1 can be chosen) as SHA-1 Certificates will no longer be created or accepted as standard in 18 months or so's time.
My solution was to generate an SHA-1 Certificate from my GoDaddy account.
All the necessary Root and Intermediate Certificated seemed to be in place but OS X Server could not correctly link up all the Certificates in the SHA-2 chain.

@heinzfromconcord were you replacing a Cert with the same name by any chance? (i.e. Were you renewing an SHA-1 Cert with an SHA-2 Cert perhaps). I have absolutely no idea whether this matters or not but can only assume that not everyone is suffering this problem as there are so few forum posts about it. I am trying to gather diagnostic information tp pass on to the Apple Engineers who replied "cannot reproduce" to my bug report.

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