I had this issue EVERY time I tried to set up and install the Emustation. I did exactly as the instructions said, downloaded everything I needed, ftp-ed across everything, and then EVERY time, Fatal Error.
The way I resolved it, was to use XBMC4Gamers, use the URLDownloader on that, and install Emustation from there. For whatever reason, it works that way. It loaded fine and I was able to set it up and so on. It just refused to work via the PC/FTP way. And after all that, I've customised the XBMC4Gamers look and style and decided to keep that as my main anyway. It still loads the emulators and that was a secondary function for me anyway. Xbox Games was the main one.