Permissions issues (dashboard widgets remain)

Hi. This issue occurs when activating my base theme which I use as a framework for sites. Before this, using the same plugins the issue does not occur. I believe it is likely to do with my functions-setup.php. This file runs once when first activating the theme. There is a section that deals with user permissions. I don't quite see how this would be effecting form permissions but it seems the most likely candidate.

Thanks

/*////////////////////////////////////////////////////////////
If needed to run functions again chnage uncommend below
////////////////////////////////////////////////////////////*/
//update_option( 'theme_setup_status', '0' );

/*////////////////////////////////////////////////////////////
Run on first theme switch
////////////////////////////////////////////////////////////*/
add_action( 'after_setup_theme', 'the_theme_setup' );

function the_theme_setup()
{
	// First we check to see if our default theme settings have been applied.
	$the_theme_status = get_option( 'theme_setup_status' );
	// If the theme has not yet been used we want to run our default settings.
	if ( $the_theme_status !== '1' ) {
/*////////////////////////////////////////////////////////////
Setup Default WordPress settings
////////////////////////////////////////////////////////////*/
		$core_settings = array(
			'avatar_default'				=> 'mystery',					// Comment Avatars should be using mystery by default
			'avatar_rating'					=> 'G',							// Avatar rating
			'comment_max_links'				=> 0,							// We do not allow links from comments
			'comments_per_page'				=> 20							// Default to 20 comments per page
		);
		foreach ( $core_settings as $k => $v ) {
			update_option( $k, $v );
		}
/*////////////////////////////////////////////////////////////
Delete dummy post, page and comment.
////////////////////////////////////////////////////////////*/
		wp_delete_post( 1, true );
		wp_delete_post( 2, true );
		wp_delete_comment( 1 );

/*////////////////////////////////////////////////////////////
Add pages
////////////////////////////////////////////////////////////*/
	$new_page_title = array ('Home','Contact','About');
	$new_page_content = array ('');
	$new_page_template = array (''); //Template, blank for default

	foreach ( $new_page_title as $page_title ) {

		$page_check = get_page_by_title($page_title);
		$new_page = array(
			'post_type' => 'page',
			'post_title' => $page_title,
			'post_content' => $new_page_content,
			'post_status' => 'publish',
			'post_author' => 1,
		);
		if(!isset($page_check->ID)){
			$new_page_id = wp_insert_post($new_page);
			if(!empty($new_page_template)){
				update_post_meta($new_page_id, '_wp_page_template', $new_page_template);
			}
		}

	}//end foreach
/*////////////////////////////////////////////////////////////
set page as front page
////////////////////////////////////////////////////////////*/
	$homeSet = get_page_by_title( 'Home' );
	update_option( 'page_on_front', $homeSet->ID );
	update_option( 'show_on_front', 'page' );

/*////////////////////////////////////////////////////////////
Change permalink structure
////////////////////////////////////////////////////////////*/
global $wp_rewrite;
    $wp_rewrite->set_permalink_structure( '/%postname%/' );

/*////////////////////////////////////////////////////////////
Remove wordpress roles
////////////////////////////////////////////////////////////*/
remove_role( 'author' );
remove_role( 'contributor' );

/*////////////////////////////////////////////////////////////
Set role capabilities
////////////////////////////////////////////////////////////*/
$edit_editor = get_role('editor');

$edit_editor->add_cap('add_users');
$edit_editor->add_cap('create_users');
$edit_editor->add_cap('delete_users');
$edit_editor->add_cap('edit_users');
$edit_editor->add_cap('list_users');
$edit_editor->add_cap('promote_users');
$edit_editor->add_cap('remove_users');

$edit_editor->add_cap('edit_theme_options');

$edit_editor->remove_cap('manage_links');

/*////////////////////////////////////////////////////////////
Set theme_setup_status as 1
////////////////////////////////////////////////////////////*/
		update_option( 'theme_setup_status', '1' );
		$msg = '
		<div class="error">
			<p>The ' . get_option( 'current_theme' ) . 'theme has changed your WordPress default <a href="' . admin_url() . 'options-general.php" title="See Settings">settings</a> and deleted default posts & comments.</p>
		</div>';
		add_action( 'admin_notices', $c = create_function( '', 'echo "' . addcslashes( $msg, '"' ) . '";' ) );

	}
	elseif ( $the_theme_status === '1' and isset( $_GET['activated'] ) ) {
		$msg = '
		<div class="updated">
			<p>The ' . get_option( 'current_theme' ) . ' theme was successfully re-activated.</p>
		</div>';
		add_action( 'admin_notices', $c = create_function( '', 'echo "' . addcslashes( $msg, '"' ) . '";' ) );
	}
}