Windows and UNIX have different style line endings. If you run this under Win32 but use a file with UNIX-style endings, the whole file will be slurped instead of processed line by line. Try this before opening your file:

use Getopt::Long;
my $line_ending = "\012"; #unix style default
GetOptions( 'windows' => sub { $line_ending = "\015\012" } );
local $/ = $line_ending;
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This will cause your script to assume UNIX line endings, but if you pass the parameter --windows to the command line, it will then assume the file has Windows-style line endings.

You could autodetect this, too, but it involves opening the file and reading until you find one of those pairs, then resetting the filehandle. I know I've seen code for that on PerlMonks...