the ideal application for web design, and I've always advised people to steer clear of it whenever possible, in favour of FrontPage, or NetObjects fusion.
That said, you're stuck with your problem, so let's see if we can't sort it out. When you save the site to your hard drive from MS Publisher I presume that you see all the individual files, is that so? If it is, it should be possible to transfer them to your server space via an FTP application. Freeserve provide a download link to a good one called Terrapin, and it's free.
Alternatively you can use the Freeserve 'FTP my site' service to upload files from your hard drive to the server. This will mean that there's only the one index.html file in your space, and browsers will load a single instance of the banner.
Have a good look at the Freeserve help page on this
click here and come back to your thread if you still have problems. As long as you can transfer the files without zipping them you should be OK.