Search Box playing Hide and Seek

This is a simple question:

Ever since working my theme around, everything has worked beautifully. Lately though, while working on my maintenance (site off-line) page and trying to get the theme to working properly, my search box has been disappearing. I'll go into themes -> configure on the website and see that the box is unchecked, so I will check it off. It will be good for about half an hour, then disappear again.

Here is where it pops up in my page.tpl.php:

<div id="navigation" class="menu<?php if ($primary_links) { print " withprimary"; } ?> ">
        <?php if (!empty($primary_links)): ?>
          <div id="primary" class="clear-block">
            <?php print theme('links', $primary_links); ?>
          </div>
        <?php endif; ?>

        <?php print $search_box; ?>


</div> <!-- /navigation -->

It may not look like it makes sense to you, but I feel like it should work perfectly, and it has up until recently. I haven't made any changes to the search feature that I can recall, so this is kind of strange to me. I searched around the site and couldn't find too much to help me out with this, so figured I'd ask.

Hope I gave enough info, and I hope this isn't something that makes me seem too stupid!