Stuart, the turnkey-make-ssl-cert with the --csr option produces three files, a certificate request, a temporary cert you can use while you wait for the real cert, and a .key file to be used with both the .csr and .crt.  Jeremy's instructions told you to look for the .crt file which is the temporary cert.  Look for the .csr file in the same directory, or run it again with the --out option.

# turnkey-make-ssl-cert -o example.com -r www.example.com
# ls
example.com.crt  example.com.csr  example.com.key

# head -1 example.com.*
==> example.com.crt <==
-----BEGIN CERTIFICATE-----

==> example.com.csr <==
-----BEGIN CERTIFICATE REQUEST-----

==> example.com.key <==
-----BEGIN PRIVATE KEY-----

Please try submitting the .csr file and let us know it that works.  Sorry for the confusion.