This can have many causes, ranging from incorrect uploading or file permissions to syntax errors within the script.
1. Make sure you upload scripts in ASCII mode, not binary. If your FTP program is set to "auto-detect," make sure that the file type (.cgi or .pl) of the script is on the list of ASCII file types.
2. Make sure that the path to PERL is correct.
3. Make sure the permissions on both the script, any files it may use, and the cgi-bin/directory are all correct. Most Perl scripts require that you CHMOD them to 755. Files that need to be written to must be CHMOD 666 or 777.
4. Check the modifications you've made to the script, as you may have introduced syntax errors. Remember to escape special characters (such as @ or $) with a backslash \ if they're in double quoted strings. Compare your edited script with the un-edited original to see if there are any errors.
If none of these things helped, we can provide support for it, although you will have to pay a fee.