simple press is not removing your footer, per se… you have javascript errors which is stopping processing of the page on your site…
this is due to something on your site, theme or plugin, misbehaving… My guess would be s2 member, but cannot be sure…
something is loading this:
<script type=’text/javascript’ src=’https://ajax.googleapis.com/ajax/libs/jquery/1.6.4/jquery.min.js?ver=latest’></script>
<script type=’text/javascript’ src=’http://ajax.googleapis.com/ajax/libs/jqueryui/1.8.16/jquery-ui.min.js?ver=3.4.1′></script>
that loads jquery and jquery ui from google instead of using the versions that come with wp… of course, plugins expect the versions that come with wp… and the jquery version loaded is quite old compared to the wp version…
please read: http://codex.simple-press.com/codex/faq/troubleshooting/what-is-this-jquery-conflict/
I am guessing s2 because both outputs in the head tags are right before additional s2 items… but could be something else… might be worth quick switch to the default wp theme and see if still occurring… does s2 offer any options to use the wp version instead of its own versions?