djripraw

Here is my fix for it.

I may have missed something so please check

// Remove default categories/taxonomies boxes //
add_action( 'admin_menu' , 'remove_default_categories_box' );
function remove_default_categories_box() {
	$options = get_option('aCategory');

	foreach($options as $taxonomy){
		$tax = get_taxonomy($taxonomy->slug);
		$catSlug = $taxonomy->slug;
		$catBox = $catSlug.'div';
		$postType = $tax->object_type;
		foreach ( $postType as $runPostType ):
			if($taxonomy->replace == 1) remove_meta_box( $catBox, $runPostType, 'side' );
		endforeach;
	}
}

// Add categories/taxonomies custom boxes //
add_action( 'add_meta_boxes', 'add_aCategories_box' );
function add_aCategories_box(){
	global $wpdb;

	if (isWPMU()) $options = get_blog_option($wpdb->blogid, 'aCategory');
	else $options = get_option('aCategory');

	foreach($options as $taxonomy){
		$tax = get_taxonomy($taxonomy->slug);
		$catSlug = $taxonomy->slug;
		$catBox = 'a-'.$catSlug;
		$postType = $tax->object_type;
		foreach ( $postType as $runPostType ):
			if($taxonomy->replace == 1) add_meta_box( $catBox, $tax->labels->name, 'aCatSelect', $runPostType, 'side', 'core', array( 'catSlug' => $catSlug, 'options' => $taxonomy));
		endforeach;
	}
}

Unfortunately not. I need it to be an automatic progress.