No, sorry.
/home/user-data/ssl would be for box.mydomain.com and /home/user-data/ssl/mydomain.com would be for mydomain.com.
The other likely problem is that you aren’t including all of the intermediate certs. I think StartSSL provides two intermediate certs, which would mean you need to paste three things into the control panel. The order of the two intermediate certs you’d have to guess / try both ways.