The issue may have to do with the way newlines are handled in Windows. First see what happens if you read and write the entire file at once rather than line by line:

undef $/;
my $content = <$MASTER>;
print $CONFIG $content;
[download]

If that works fine, my theory is probably right. If you do still want to use line-by-line transfer, I believe you can add :unix to the layers on your open calls.