Maybe you're printing the file before your header:

      # (Your print stuff)
      open (FILE, "..."); # ...

      my ($cgi) = new CGI;
      print $cgi->header;
[download]

In this case, the CGI will not output a valid header, instead showing the contents of your file. An invalid header is grounds for a 500 error.

Note that if you run your script on the command line, it will "work" fine, in as much as it runs, but it will not output the proper header for your Web server.

For debugging this kind of thing, you absolutely must use CGI::Carp. It's not optional. It will log all errors to your error_log instead of them being lost in the great void.