Pagination adding "index.php" into pagination links after category name

Question

My question is similar to this one, but since it is different enough and has no accepted answers yet, I am posting my question as well. I have a very simple listing page by category with pagination. I am removing "index.php" from the URL's via .htaccess using the code from EllisLab.

When on this page: /products/category/coins, the pagination links are /products/category/coinsindex.php/P60 and /products/category/coinsindex.php/P120.

Where is the extra "index.php" coming from?

Here is my code:

{paginate}
{pagination_links}
<ul class="pagination">
    {first_page}<li class=""><a href="{pagination_url}" class="page-first">First</a></li>{/first_page}
    {previous_page}<li><a href="{pagination_url}" class="page-previous arrow">&laquo;</a></li>{/previous_page}
    {page}<li {if current_page}class="current unavailable"{/if}><a href="{pagination_url}" class="page-{pagination_page_number}">{pagination_page_number}</a></li>{/page}
    {next_page}<li><a href="{pagination_url}" class="page-next arrow">&raquo;</a></li>{/next_page}
    {last_page}<li class=""><a href="{pagination_url}" class="page-last">Last</a></li>{/last_page}
</ul>
{/pagination_links}

{/paginate}

Any help would be greatly appreciated!

Answer 1

You should remove "index.php" from 'Name of your site's index page' in control panel (Admin -> General configuration).

Answer 2

The problem was an EE bug. I upgraded and the problem went away. Thanks to Bluedreamer for the comment which gave me the solution.