put this into a test php file:

<?php
	$temp = "this is\n\na test\n";
	printf("%s", nl2br($temp));
?>

and you should get this as output from your webserver:

this is<br />
<br />
a test<br />

I have confirmed this to be also an issue in the 4.0.6 release candidates, but I do not know when this all of a sudden became an issue.  I'd like to know why it's creating <br /> tags instead of <br> tags :)