It's caused by loading <style type="text/css">#wp-content-wrap { display:none; }</style> with template.
This cause disappearing of content box.
There is wp_editor(...) also loading, i don't know what for. May be Hiroaki will explain.
This code locates in custom-field-template.php (Version: 2.0.2) lines 2620-2625.
if (substr($wp_version, 0, 3) >= '3.3' && !post_type_supports($post->post_type, 'editor') && $post->post_type != 'post' && $post->post_type != 'page') :
wp_editor('', 'content', array('dfw' => true, 'tabindex' => 1));
$out = '<style type="text/css">#wp-content-wrap { display:none; }</style>';
else :
$out = '';
endif;
Delete this code and content will not disappear next time you load template.