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I also think you've missed this part of the installation instructions:
"If your running in a hosted environment, unpack the XOOPS 2 files locally or on the server if you have telnet or SSH access. Once you done this, make sure to
move or copy all XOOPS 2 files from the HTML directory to your root web directory (your provider usually provides this location with directions). Once the files are copied there, you can start the install by typing
http://yoursite.com. This will start the install process."
In short, you were not supposed to include the HTML directory itself, only its contents. Some users encountered problems because of this.