marblecake

I had the same issues with checkboxes. Needed hierarchical taxonomy checkboxes, so edited taxcheckbox.php and replaced the foreach loop with this:

$parents = array();
$children = array();

foreach($terms as $term){
	if($term->parent == 0){
		$parents[] = $term;
	}else{
		if(!isset($children[$term->parent])){
			$children[$term->parent] = array();
		}
		$children[$term->parent][] = $term;
	}
}

foreach($parents as $parent){

	if(isset($_GET['taxo'][$c]['term'])){
		if(is_array($_GET['taxo'][$c]['term']) ){
			$selected = (isset($_GET['taxo'][$c]['term']) && in_array($parent->slug, $_GET['taxo'][$c]['term'])) ? 'checked="checked"' : '';}
		else{
			$selected = (isset($_GET['taxo']) && $_GET['taxo'][$c]['term']==$parent->slug) ? 'checked="checked"' : '';
		}
	}

	$value = $parent->slug;
	echo '<label class="taxcheckbox"><input type="checkbox" id="taxo-'.$c.'" name="taxo['.$c.'][term][]" value="'.$value.'" '.$selected.'>'.$parent->name.'</label>';

	if(isset($children[$parent->term_id])){

		echo '<ul class="taxcheck-children">';

		foreach($children[$parent->term_id] as $child){
			if(isset($_GET['taxo'][$c]['term'])){
				if(is_array($_GET['taxo'][$c]['term']) ){
					$selected = (isset($_GET['taxo'][$c]['term']) && in_array($child->slug, $_GET['taxo'][$c]['term'])) ? 'checked="checked"' : '';}
				else{
					$selected = (isset($_GET['taxo']) && $_GET['taxo'][$c]['term']==$child->slug) ? 'checked="checked"' : '';
				}
			}

			$value = $child->slug;
			echo '<li><label class="taxcheckbox"><input type="checkbox" id="taxo-'.$c.'" name="taxo['.$c.'][term][]" value="'.$value.'" '.$selected.'>'.$child->name.'</label></li>';
		}

		echo '</ul>';

	}

}