The above works find on Windows - Are you using a Cygwin build?

I'm running the program under plain Windows at the moment...

But programming is a black art, really. When I came back to work today, with some ideas how to test it, I found that the program runs fine, without any modifications - no extra \r anymore on output! Of course I still had the bug of extra \n, because of the way I read in my data, but this was trivial to correct. In short: I have no idea why it didn't work yesterday, but works well today. Creepy.

For completeness, here is the full code (unmodified) which I'm using to test. In particular, I did not yet try the (neat) idea of using raw mode. It turned out to be unnecessary in this case:

use strict;
use warnings;
use IO::File;

# copy \n delimited file from Windows to
# Samba share on Unix. Output is also 
# supposed to be delimited by \n
my $par='c:/tmp/dev.cs';
my $file=new IO::File $par,'r' or die "$!";
my $data=join '',<$file>; # !!!!
undef $file;
my $_path_local='u:/transfer/devc.cs';
my $handle=IO::File->new($_path_local,'w') or die "$!";
$handle->binmode;
print $handle $data;
$handle->close;
[download]

My best explanation for the fact that it suddenly turned out to work overnight is that I mistakingly grabbed an old version of my application from our source control system (a version which did not have the binmode set), and used *that* one instead of the version I had in my editor. Not likely, but the best explanation aside from a miracle having happened.

Thank you to everyone for contributing ideas.