>> More specifically, have got one .pem file, CA_Roots.pem, with a whole bunch of X.509 certificates in it .. which I thought I needed.
that pem file is not used by a server, only a client.
the certificate you need to worry about is in your certificates folder.
>> My .crt file has a primary and secondary intermediate cert text in addition to the base one.
yes, that's the file you want to be looking into. I read it that you have too many, or not enough, intermediate certificates in there.
cheers
Bruce