... a problem with Windows files used under Unix ...

If this is certain to be the situation, I think I would take the approach of local-ly changing  $/ (see perlvar) to  "\x0d\x0a" to control both the reading of Windoze-ish lines from a filehandle and the behavior of chomp in removing their line-enders. Something like:

open my $fh ... or die ...;
...
{
    local $/ = "\x0d\x0a";
    while (defined(my $line = <$fh>)) {
        chomp $line;
        do_something_with($line);
        }
}
[download]

Both problems handled in one swell foop. (Of course, you have to be aware that the change to the global  $/ propagates 'into' the  do_something_with() call and into anything that function may call, but that's a post for another day.)