In the prosilver ucp_footer.html template file, jumpbox.html is included prior overall_footer.html. Since the jumpbox dropdown doesn't display in User Control Panel, even if it's enabled in ACP (board features), I assume the goal is displaying an upper margin for navbar footer...
However, jumpbox.html is NOT included in mcp_footer.html, and some other files such as search_body.html. Therefore, unlike ucp_footer.html, there is no margin above navbar footer in Moderator Control Panel. Same applies to Advanced Search (search_body.html) compared to Search results (search_results.html) where there are no displayed jumpbox and recent searches, for example.
You should either include jumpbox.html in mcp_footer.html and other places or simply remove the space <br /><br /> inside jumpbox.html when there is no displayed jumpbox and thus remove jumpbox.html in ucp_footer.html because it's apparently useless except for that margin.