Are you using the quote entity instead of the double quote like the code you posted here:
php:
<?php if(WA_Auth_RulePasses("Logged in to users"){ // Begin Show Region ?>
<a href="../Admin/contents_search.php">Advanced Search</a> | <a href="../admin/users_logout.php">Log Out</a>
<?php } // End Show Region ?>
If so you should update it to use the double quote characters like this:
php:
<?php if(WA_Auth_RulePasses("Logged in to users"){ // Begin Show Region ?>
<a href="../Admin/contents_search.php">Advanced Search</a> | <a href="../admin/users_logout.php">Log Out</a>
<?php } // End Show Region ?>
