Make sure your permissions are correct as indicated in the readme for the script you arte installing. Most importantly, you must use forced ASCII FTP upload. Go into your settings on your FTP client and make sure you have "use ASCII" or something similar checked. DO NOT use Auto or binary for .cgi, .txt, .pl. I do not know why autodetect does not upload them properly, but this is how I got scripts working on my box (that and creating a new i-bay to use other than Primary).
Hope this helps,
Derek Godfrey