I just tried putting both certificates back into one file and uploading it just to the certificate, then I tried uploading the same file to both the certificate and ca certificate, but it’s still showing the same thing on SSL shopper, and now my ca Certificate shows both parts in it on GoDaddy. 
Could GoDaddy be someone doing something to change the version of the CA Cert it’s passing off? So frustrating! Arg and I have a year to go with them too.