You should add e.g. the following code:
Code:
{if $per_page eq "Y" and $total_items gte $per_page_values.0}
{include file="customer/main/per_page.tpl"}
{/if}
to the "skin/common_files/customer/search_sort_by.tpl" template.
And comment out the per_page.tpl reference in the "skin/common_files/customer/main/navigation.tpl" template:
Code:
{*include file="customer/main/per_page.tpl"*}