Index: includes/form.inc
===================================================================
RCS file: /cvs/drupal/drupal/includes/form.inc,v
retrieving revision 1.461
diff -u -p -r1.461 form.inc
--- includes/form.inc	7 May 2010 14:48:10 -0000	1.461
+++ includes/form.inc	9 May 2010 18:00:47 -0000
@@ -1291,6 +1291,13 @@ function form_builder($form_id, $element
   // Recurse through all child elements.
   $count = 0;
   foreach (element_children($element) as $key) {
+    // Prior to checking properties of child elements, their default properties
+    // need to be loaded.
+    if (isset($element[$key]['#type']) && empty($element[$key]['#defaults_loaded']) && ($info = element_info($element[$key]['#type']))) {
+      $element[$key] += $info;
+      $element[$key]['#defaults_loaded'] = TRUE;
+    }
+
     // Don't squash an existing tree value.
     if (!isset($element[$key]['#tree'])) {
       $element[$key]['#tree'] = $element['#tree'];
@@ -1312,12 +1319,6 @@ function form_builder($form_id, $element
     $array_parents[] = $key;
     $element[$key]['#array_parents'] = $array_parents;
 
-    // Prior to handling #weight, default element properties need to be applied.
-    if (isset($element[$key]['#type']) && empty($element[$key]['#defaults_loaded']) && ($info = element_info($element[$key]['#type']))) {
-      $element[$key] += $info;
-      $element[$key]['#defaults_loaded'] = TRUE;
-    }
-
     // Assign a decimal placeholder weight to preserve original array order.
     if (!isset($element[$key]['#weight'])) {
       $element[$key]['#weight'] = $count/1000;
Index: modules/system/system.module
===================================================================
RCS file: /cvs/drupal/drupal/modules/system/system.module,v
retrieving revision 1.927
diff -u -p -r1.927 system.module
--- modules/system/system.module	6 May 2010 15:21:25 -0000	1.927
+++ modules/system/system.module	9 May 2010 18:00:56 -0000
@@ -383,7 +383,6 @@ function system_element_info() {
   );
   $types['checkboxes'] = array(
     '#input' => TRUE,
-    '#tree' => TRUE,
     '#process' => array('form_process_checkboxes'),
     '#theme_wrappers' => array('checkboxes'),
     '#pre_render' => array('form_pre_render_conditional_form_element'),