Not to beat a dead horse or anything but I was able to recreate your problem using Mac OSX 10.2.8 using BBEdit_Lite 6.1. However, the same script when created with vi ran just fine. I opened up the one created in BBEdit with vi and saw the ^M characters had munged the whole works. Also, I turned on warnings and got the following message:

bash-2.05a$ comment.pl
use: bad interpreter: No such file or directoryerl

So the problem is the line endings. There are a couple of ways to clean it up. One (unfortunately not available with OSX version of *nix) is the "unix2dos" command. The other method would be to do some sort of Perl (or sed) script to clean up the control characters. I think if you switch \015 (control-M or Carriage Return) for say \012 (control-L or Line Feed), you should be ok. Something along the lines of say:

#!/usr/bin/perl

use warnings;
use strict;

my $in=$ARGV[0];
my $out=$ARGV[1];

open IN, "$in" or die "Can't do it man. $!";
open OUT, ">>$out" or die "Man, I can't do that. $!";
foreach (<IN>) {
 s/\015/\012/g;
 print OUT $_;
 }
close IN;
close OUT;
exit;
[download]

I tried this out and it should do the trick. HTH

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"Ex libris un peut de tout"