My setup is Debian-Etch, I used the perfect setup. I added a new user and site in ispconfig, when I upload some files they went to /var/www/web1/user/web1_username/web instead of /var/www/web1/web can someone tell me what I did wrong?
Make sure that you set the user that you are using to login with the FTP as admin! If not (as you did now), you will upload the files to the personal folder / site. Only the user as admin can upload file to the root of the domain (/var/www/web1/web)