Keep in mind that Fake LE Intermediate X1 is not the same as Let’s Encrypt Authority X1.
When you issue a certificate on Let's Encrypt staging server, your certificate is always signed by Fake LE Intermediate X1 so you receive a certificate signed by this fake CA and the intermediate CA certificate that is Fake LE Intermediate X1.
When you issue a certificate on Let's Encrypt production server, your certificate is always signed by Let’s Encrypt Authority X3 (right now, it could change in a future) so you receive a certificate signed by this CA and the intermediate CA certificate that is Let’s Encrypt Authority X3.
Let’s Encrypt Authority X1 was the production intermediate certificate for Let's Encrypt but it is not in use since 16th March 2016 that is the reason I said that if you see that the intermediate CA for your production cert signed by Let’s Encrypt Authority X3 is shown as Let’s Encrypt Authority X1 something really wrong is going on there.
Cheers,
sahsanu