Kim:
Your Template is probably missing the proper "switches" to turn them on and off - Suggest you compare your tpl_main_page.php to one from the template default.
Had thought that initially, and they looked the same. However, to be sure, i just compared them with Winmerge and they're identical. To be extra sure, i compared my template with an unaltered download of 1.3.8a afterwards and they're still identical. Am i right in thinking i should compare includes/templates/MYTEMPLATE/templates/tpl_index_default.php?
My template file (and the default file) has the following code:
<?php if ($show_display_category->fields['configuration_key'] == 'SHOW_PRODUCT_INFO_MAIN_NEW_PRODUCTS') { ?>
<?php
/**
* display the New Products Center Box
*/
?>
<?php require($template->get_template_dir('tpl_modules_whats_new.php',DIR_WS_TEMPLATE, $current_page_base,'templates'). '/tpl_modules_whats_new.php'); ?>
<?php } ?>