nginx config fails with SSL key/pem (unique case)

check here

I hope you've copy-pasted with the following lines:

-----BEGIN CERTIFICATE-----
...
-----END CERTIFICATE-----
-----BEGIN RSA PRIVATE KEY-----
...
-----END RSA PRIVATE KEY-----

A different solution that may work for others:

use the .pem file for both ssl_certificate and ssl_certificate_key

That is:

...
ssl on;
ssl_certificate      conf.d/cert.pem;
ssl_certificate_key  conf.d/cert.pem;
...

FYI, make sure your BEGIN block is identical to the expected block, character for character. Mine started with 4 dashes, not 5. ---- vs -----. The validation tooling error messages aren't very specific when you make this error.