If it's a problem with different line endings in a text file between unix and win32, you could open the file using the :crlf layer. For example, this script:

use strict;
use warnings;
open(my $fh, '<', 'test.txt') or die $!;
my $count = 0;
while (<$fh>) {
  $count++ if /\r/;
}
close $fh;
print "Without :crlf, \$count=$count\n";

open($fh, '<:crlf', 'test.txt') or die $!;
$count = 0;
while (<$fh>) {
  $count++ if /\r/;
}
close $fh;
print "With :crlf, \$count=$count\n";
[download]

will print out on a unix machine, for a 10-line file test.txt created on Win32,

Without :crlf, $count=10
With :crlf, $count=0
[download]