Can you check the format of the certificate? 
I have similar issues and in my case the certificate (and the chain) have the 
subject in printable format. FreeIPA issues the CSR with UTF and thus there is 
a mismatch. 
You can check the certificate like this:

openssl x509 -in ca-certificate.pem -subject -issuer -nameopt 
multiline,show_type -noout -subject_hash -issuer_hash
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