I must be doing something stupid. Here's my little test program:

#!/usr/bin/perl

use v5.10 ;
use strict;
use warnings ;

my $BOM  = "\xef\xbb\xbf" ;

die "no args\n" unless @ARGV == 2 ;
open (my $i, "<", $ARGV[0]) or die "Can't open $ARGV[0]\n" ;
open (my $o, ">", $ARGV[1]) or die "Can't write to $ARGV[1]\n" ;
say "marker is" ;
printhex ($BOM) ;
say "" ;
while (my $line = <$i>)
{   my $newline = $line ;
    printhex ($newline) ;
    $newline =~ s/$BOM//g; 
    die "didn't change" if $newline eq $line ;
    print $o $newline ; 
}
close $i ;
close $o ;
exit ;

sub printhex
{   my $str = $_[0] ;
    for my $chr (split(//,$str))
    {   printf("%x ", ord($chr)) ; }
}
[download]

and when I run it on one of teh BOM'ed files I get:

marker is
ef bb bf
didn't change at D:\Desktop\striputf.pl line 19, <$i> line 3.
ef bb bf 49 6d 70 6f 72 74 61 6e 63 65 2c 46 69 72 73 74 20 4e 61 6d 6
+5 2c 4d 69 64 64 6c 65 20 4e 61 6d 65 2c 4c 61 73 74 20 4e 61 6d 65 2
+c 46 75 6c 6c 20 4e 61 6d 65 2c 43 6f 6d 70 61 6e 79 2c 44 65 70 61 7
+2 74 6d 65 6e 74 2c 4a 6f 62 20 54 69 74 6c 65 2c 53 74 72 65 65 74 2
+0 28 62 2e 29 2c 43 69 74 79 20 28 62 2e 29 2c 53 74 61 74 65 20 28 6
+2 2e 29 2c 5a 49 50 20 43 6f 64 65 20 28 62 2e 29 2c 43 6f 75 6e 74 7
+2 79 2f 52 65 67 69 6f 6e 20 28 62 2e 29 2c 48 6f 6d 65 20 50 68 6f 6
+e 65 2c 42 75 73 69 6e 65 73 73 20 50 68 6f 6e 65 2c 4d 6f 62 69 6c 6
+5 20 50 68 6f 6e 65 2c 42 75 73 69 6e 65 73 73 20 50 68 6f 6e 65 20 3
+2 2c 42 75 73 69 6e 65 73 73 20 50 68 6f 6e 65 20 33 2c 42 75 73 69 6
+e 65 73 73 20 50 68 6f 6e 65 20 34 2c 42 75 73 69 6e 65 73 73 20 46 6
+1 78 2c 42 75 73 69 6e 65 73 73 20 57 65 62 20 50 61 67 65 2c 53 74 7
+2 65 65 74 20 28 68 2e 29 2c 43 69 74 79 20 28 68 2e 29 2c 53 74 61 7
+4 65 20 28 68 2e 29 2c 5a 49 50 20 43 6f 64 65 20 28 68 2e 29 .....
[download]

What am I getting wrong/missing?