I've just uploaded a new site on C5 5.6 with the Slate theme, but there are two issues:

One is that all landing pages show site.com/index.php/contact/ instead of site.com/contact/

The other is there is a block of footer links that displays perfectly when logged in and editing but when it goes live they are not visible. The footer.php files shows this code for the footer items (below) but they are empty when published. I don't know how they can disappear between preview and live. I've cleared the cache multiple times.

Relevant portion of footer.php
<footer>
<div class="row">
<div class="col_3">
<?php
$a = new GlobalArea('Footer');
$a->display();
?>
</div><!-- .col_3 ends -->
<div class="col_3">
<?php
$a = new GlobalArea('Footer Column Two');
$a->display();
?>
</div><!-- .col_3 ends -->
<div class="col_3">
<?php
$a = new GlobalArea('Footer Column Three');
$a->display();
?>
</div><!-- .col_3 ends -->
<div class="col_3 last">
<?php
$a = new GlobalArea('Footer Column Four');
$a->display();
?>
</div><!-- .col_3 ends -->
</div><!-- .row ends -->

------------
This is the source when its live:

<footer>
<div class="row">
<div class="col_3">
</div><!-- .col_3 ends -->
<div class="col_3">
</div><!-- .col_3 ends -->
<div class="col_3">
</div><!-- .col_3 ends -->
<div class="col_3 last">
</div><!-- .col_3 ends -->
</div><!-- .row ends -->