What's the URL of your site so we can examine it first hand? If your website is missing some files after being published to your new host server then the upload process has not uploaded all of the files.
You can tell which files are missing by bringing up the Activity window (Command+Option+A) for the site in Safari and check the list of files.
Try using the File ➙ Publish Entire Site menu option to force a full publication of all the site's files. See if that will get all of the files uploaded properly.
All three apps use Finder like windows of your server folder that facilitates simple drop and drag of files from your hard drive to the server for manual uploading.