Yes, that appears to be the problem. 
We have not confirmed it yet with the customer, but tests we did with a test 
root-ca (openssl) did show that the certificate needs to have the same order of 
the DN components as the csr in order for FreeIPA to accept it.

Our tests also showed that we can set the order on both sides, meaning that the 
FreeIPA server accepted the certificate if it was signed with 
(FreeIPA and NSS)
CSR: CN,O,C
CERT: CN,O,C
and 
(OpenSSL)
CSR: C,O,CN
CERT: C,O,CN

The order of the values can be configured on either the FreeIPA server when 
creating the csr by rearanging the order of the DN components or 
on the root-ca end with modifying the configuration file openssl uses:

[ policy_anything ]
countryName             = optional
stateOrProvinceName     = optional
localityName            = optional
organizationName        = optional
organizationalUnitName  = optional
commonName              = supplied
name                    = optional
emailAddress            = optional

Thanks,
Anestis
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