The Intuitive Category Checklist plugin for WordPress is great when you have a lot items in a hierarchical taxonomy box, such as the categories box. The plugin will allow you to expand and collapse a parent with sub-categories. The problem arises with how the plugin handles the boxes containing the taxonomies. First it removes the boxes, then it loops through the content and creates an entirely new box. This is fine except that it ignores any box which is not a hierarchical taxonomy box. Those to not get removed and re-added. The newly re-added boxes are added with a higher priority than the non-taxonomy boxes and therefore show above them. It is an easy fix. Simply crack open the intuitive-category-checklist.php file and, locate line 38 and change it from:
add_meta_box($tax_name . 'div', $label, 'icc_taxonomy_meta_box', $post_type, 'side', 'high', array('taxonomy' => $tax_name));
add_meta_box($tax_name . 'div', $label, 'icc_taxonomy_meta_box', $post_type, 'side', 'default', array('taxonomy' => $tax_name));
Refresh your post page an viola! You Publish box will be back on top. Now remember, if you had added any custom boxes of your own with specific locations this plugin will ignore them and set it to the default location. Maybe somebody knows how to find where the current boxes are and will patch the code in the future.