includes/modules/pages/checkout_one_confirmation/header_php.php line 129 is
Code:
$_SESSION['comments'] = (zen_not_null ($_POST['comments'])) ? zen_clean_html ($_POST['comments']) : '';
Do you think the call to zen_clean_html is absolutely required? I'm asking because I don't think the standard checkout does this operation.

In the standard checkout, a comment entry like:

line1
line2
line3

has the line breaks preserved, but in OPC, because of the zen_clean_html operation, they are all put on one line.