Please try the follwing: edit the "skin/common_files/modules/One_Page_Checkout/profile/address_fields.tpl" template and add this code
Code:
{if $ex_additional_address_fields ne ''}
<li class="clearing"></li>
{/if}
right after this code fragment
Code:
{include file="main/additional_address_fields.tpl" ex_additional_address_fields=$ex_additional_address_fields require_aid='Y' ex_list_view='Y'}