Is the client publishing via http://www.example.com or using FTP? Usually when you publish with http, FP will put the files in the correct place. If you use FTP, FP will rely on the user to possibly enter a folder name. Make sure he is not publishing to http://www.example.com/public_html as well.
Also, if the user has any FP component (especially forms), the user needs to publish with http - FTP will not work and can corrupt the extensions.
Chances are, you might need to set up the FPSE on the server - setting up the authoring control and the default email server.
CoreyMicrosoft Expression Web BlogMy Merchant Account Blog