Whatever you do, don't use binmode on your textfile handle. You'd prevent conversion of "\n" to the proper line ending for your platform, in this case CR+LF, and which might make notepad fail to see a it, as it'd still be a bare LF.

Oh, one more idea. Could it be that your file contains extra "\r" characters? There shouldn't be any at all. You see, notepad, and anything else using the same textbox control, use CR+CR+LF as a flag for soft wrap. Change anything in your text and they all disappear. That's why it's possible to download a text file from the internet, a HTML file for example, try to edit one tiny thing, and end up with just one huge line for the whole file. Downloaded HTML files often contain two CR characters per LF, and notepad strips them all.

This snippet can delete them all for you, if present:

tr/\r//d;
[download]

Like I said, without binmode, Perl will convert the normal "\n" characters to the proper CR+LF combinations. Start with CR+LF, and you'll get CR+CR+LF.