place <?php endif; ?>
after second ul like below
<?php if ($this->session->userdata('is_logged_in') != 0): ?>
<ul class="nav navbar-nav navbar-right">
<li><a href="<?php echo base_url('auth/register');?>">Register</a></li>
<li><a href="<?php echo base_url('auth/login');?>">Sign In</a></li>
</ul>
<?php endif; ?>
you are using Tank_Auth so you should use blow code to check user logged in
$this->tank_auth->is_logged_in()