One thing to note is that the Qualys SSL Labs test will complain if your server sends the (self-signed) root CA certificate, which will already be in the end-user's trust store. This uses unnecessary bandwidth for every TLS negotiation.

In many cases, the CA (or company you got your certificate from) will include this root cert in the chain. With most web servers it is perfectly fine to simply remove it, but I have seen applications where you cannot (VMware, which wants a complete chain ending with a self-signed cert) and where you'll have to ignore the SSL Labs warning.