It's possible the files are going to the wrong place on the server.
When you log in via FTP normally you will default into that users HOME directory. example /home/username/ (where username is the actual username) If you are uploading to this directory that is mostly likely wrong.
A directory should exist for your domain name /home/user/domainname.com that you should change into.
The above assumes that you are using the correct FTP user for the domain. You can verify which "user" controls a domain by looking on the manage domains page of the panel.