WP with Bootstrap tutorial weird thing

I’ve finally got this very helpful tutorial on using Bootstrap in WordPress to work the way it should:

http://blog.teamtreehouse.com/responsive-wordpress-bootstrap-theme-tutorial`

But Zac Gordon says to use:

<?php wp_footer(); ?>

in ‘footer.php’, which causes the two fields at the top right – ‘login’, ’email’ and the ‘sign-in’ button to get crushed and disappear. Without adding

<?php wp_footer(); ?>

to ‘footer.php’, everything is rendering great. Mysteries like this annoy me. Without having to post it all to a live link. Can anyone please tell me why putting

<?php wp_footer(); ?>

in ‘footer.php’ crushes the two input fields and the ‘Sign-in’ button? And why leaving it out works, please?

Many thanks.

InFlight