Steve,
I had the same problem. Just comment out the following lines from catalog/shopping_cart.php.
<!--
<?php
echo TEXT_ALTERNATIVE_CHECKOUT_METHODS;
?>
</td>
</tr>
<?php
reset($initialize_checkout_methods);
while (list(, $value) = each($initialize_checkout_methods)) {
?>
<tr>
<td><?php echo tep_draw_separator('pixel_trans.gif', '100%', '10'); ?></td>
</tr>
<tr>
<td align="right" class="main"><?php echo $value; ?></td>
</tr>
-->