Unable to renew Directory Server and Apache SSL server certificates

The Directory Server and Apache SSL server certificates on our IPA master (RHEL 6.5/IPA version 3.0.0) server did not renew automatically and are now expired. I have followed the steps in How do I manually renew Identity Management (IPA) certificates after they have expired? (Master IPA Server) but these three certificates will not renew.

The error shown by

getcert list

ipa-getcert resubmit -i [Request ID]

Certificate operation cannot be completed: Failure decoding Certificate Signing Request: (SSL_ERROR_NO_CERTIFICATE) Unable to find the certificate or key necessary for authentication.).

Before resubmission, when the services have been restarted the error is more likely to be

(SEC_ERROR_BUSY) NSS could not shutdown. Objects are still in use.

Any help would be appreciated.