[Plugin: User Permissions] listed twice

Same here – how do I remove the duplicate metabox without breaking the plugin altogether?

Same problem…

You can edit the user-permissions.php code in the wp-content/plugins/user-permissions/user-permissions.php

** Make a backup first! **

near the top of the file ( ~line 31…) change the function as follows:
notice the //jwatson comment and the two following commented out lines.

class User_Permissions extends UserPermission_Plugin
{
	function User_Permissions ()
	{
		$this->register_plugin ('user-perms', __FILE__);

		$this->add_filter ('user_has_cap', 'check_capabilities', 10, 3);
		$this->add_action ('the_posts');

		if (is_admin ())
		{
                        // jwatson omit duplicate display issue
			//$this->add_action ('dbx_post_sidebar', 'edit');
			//$this->add_action ('dbx_page_sidebar', 'edit');
			$this->add_action ('edit_page_form', 'edit');
			$this->add_action ('save_post');
		}
	}