Oh, I just noticed that on the shopping cart page it's not showing the right side bar and the footer because of the code:
<!-- bof Ultimate Cross Sell Combo -->
<?php require(DIR_WS_MODULES . zen_get_module_directory(FILENAME_CART_UPSELL)); ?>
<?php require($template->get_template_dir('tpl_modules_also_purchased.php',DIR_WS_TEMPLATE, $current_page_base,'templates'). '/tpl_modules_also_purchased.php'); ?>
<!-- eof Ultimate Cross Sell Combo -->
When I take it out they reappear again.
Also, I've added a line of code (echo "test";) to each file we're requiring here on the very top - "test" is not being outputted at all. Seems like the problem lies somewhere much deeper. Thoughts?