One way that I can think of for this effect to happen, is if you are running your programs on Windows (which uses \r\n as the line end marker) but that your data is generated on some version of Unix (which uses \n). In that case, your Windows programs won't ever recognise the Unix line end characters. If this is the case then really the conversion of the line end characters should be dealt with by the file transfer mechanism (for example, using FTP in ASCII mode.

This does not seem to be the case:

C:\temp>cat -A foo.txt
foo$
bar$
baz$

C:\temp>perl -le "chomp(@a=<>);print for map qq|<$_>|, @a" foo.txt | c
+at -A
<foo>^M$
<bar>^M$
<baz>^M$
[download]

Oh, and for completeneess, the other way round:

tilde:~ [11:19:27]$ cat -A foo.txt
foo^M$
bar^M$
baz^M$
tilde:~ [11:19:47]$ perl -le 'chomp(@a=<>);print for map qq|<$_>|, @a'
+ foo.txt | cat -A
<foo^M>$
<bar^M>$
<baz^M>$
[download]