Incase anyone else stumbles across this I just installed certbot on a Debian Wheezy box with apache and had to use all three of:
SSLCertificateKeyFile /etc/letsencrypt/live/[FQDN]/privkey.pem
SSLCertificateChainFile /etc/letsencrypt/archive/[FQDN]/chain1.pem
SSLCertificateFile /etc/letsencrypt/live/[FQDN]/fullchain.pem
as without the SSLCertificateChainFile the grade was also capped at B due to a reported incomplete chain.