99% of the time this indicates that you FTP'd the file from a Windows box to a non-Windows server using "binary" mode, which leaves stray carriage returns in the file. The first line of the file probably read   #!/usr/bin/perl^M Which gets you a 500 error since there's no executable in /usr/bin named perl^M. Adding the -w changed this to   #!/usr/bin/perl -w^M which runs, since the executable is found.

Try FTPing in "text" mode next time.