Index: modules/simpletest/drupal_web_test_case.php
===================================================================
RCS file: /cvs/drupal/drupal/modules/simpletest/drupal_web_test_case.php,v
retrieving revision 1.147
diff -u -p -r1.147 drupal_web_test_case.php
--- modules/simpletest/drupal_web_test_case.php	5 Sep 2009 13:05:30 -0000	1.147
+++ modules/simpletest/drupal_web_test_case.php	10 Sep 2009 17:49:49 -0000
@@ -901,7 +901,11 @@ class DrupalWebTestCase extends DrupalTe
     $role = new stdClass();
     $role->name = $name;
     user_role_save($role);
-    user_role_set_permissions($role->name, $permissions);
+    $grants = array();
+    foreach ($permissions as $permission) {
+      $grants[$permission] = 1;
+    }
+    user_role_set_permissions($role->name, $grants);
     
     $this->assertTrue(isset($role->rid), t('Created role of name: @name, id: @rid', array('@name' => $name, '@rid' => (isset($role->rid) ? $role->rid : t('-n/a-')))), t('Role'));
     if ($role && !empty($role->rid)) {
Index: modules/user/user.admin.inc
===================================================================
RCS file: /cvs/drupal/drupal/modules/user/user.admin.inc,v
retrieving revision 1.77
diff -u -p -r1.77 user.admin.inc
--- modules/user/user.admin.inc	5 Sep 2009 15:05:05 -0000	1.77
+++ modules/user/user.admin.inc	10 Sep 2009 17:46:09 -0000
@@ -663,8 +663,7 @@ function user_admin_permissions($form_st
  */
 function user_admin_permissions_submit($form, &$form_state) {
   foreach ($form_state['values']['role_names'] as $rid => $name) {
-    $permissions = array_filter($form_state['values'][$rid]);
-    user_role_set_permissions($rid, $permissions);
+    user_role_set_permissions($rid, $form_state['values'][$rid]);
   }
 
   drupal_set_message(t('The changes have been saved.'));
Index: modules/user/user.module
===================================================================
RCS file: /cvs/drupal/drupal/modules/user/user.module,v
retrieving revision 1.1042
diff -u -p -r1.1042 user.module
--- modules/user/user.module	10 Sep 2009 12:33:45 -0000	1.1042
+++ modules/user/user.module	10 Sep 2009 17:52:17 -0000
@@ -2332,23 +2332,25 @@ function user_role_delete($role) {
  *   A boolean indicating whether to add permissions or to merge
  *   with all existing permissions.
  */
-function user_role_set_permissions($role, array $permissions = array(), $merge = FALSE) {
+function user_role_set_permissions($role, array $permissions = array()) {
   $role = user_role_load($role);
-  if (!$merge) {
-    // Delete existing permissions for the role.
-    db_delete('role_permission')
-      ->condition('rid', $role->rid)
-      ->execute();
-  }
 
   // Assign the new permissions for the role.
-  foreach ($permissions as $permission_string) {
-    db_merge('role_permission')
-      ->key(array(
-        'rid' => $role->rid,
-        'permission' => $permission_string,
-      ))
-      ->execute();
+  foreach ($permissions as $name => $value) {
+    if (!empty($value)) {
+      db_merge('role_permission')
+        ->key(array(
+          'rid' => $role->rid,
+          'permission' => $name,
+        ))
+        ->execute();
+    }
+    else {
+      db_delete('role_permission')
+        ->condition('rid', $role->rid)
+        ->condition('permission', $name)
+        ->execute();
+    }
   }
 
   // Clear the user access cache.
Index: profiles/default/default.install
===================================================================
RCS file: /cvs/drupal/drupal/profiles/default/default.install,v
retrieving revision 1.2
diff -u -p -r1.2 default.install
--- profiles/default/default.install	27 Aug 2009 20:25:29 -0000	1.2
+++ profiles/default/default.install	10 Sep 2009 17:54:11 -0000
@@ -184,15 +184,19 @@ function default_install() {
   db_insert('taxonomy_vocabulary_node_type')->fields(array('vid' => $vid, 'type' => 'article'))->execute();
 
   // Enable default permissions for system roles.
-  user_role_set_permissions(DRUPAL_ANONYMOUS_RID, array('access content'));
-  user_role_set_permissions(DRUPAL_AUTHENTICATED_RID, array('access content', 'access comments', 'post comments', 'post comments without approval'));
+  user_role_set_permissions(DRUPAL_ANONYMOUS_RID, array('access content' => 1));
+  user_role_set_permissions(DRUPAL_AUTHENTICATED_RID, array('access content' => 1, 'access comments' => 1, 'post comments' => 1, 'post comments without approval' => 1));
 
 
   // Create a default role for site administrators, with all available permissions assigned.
   $admin_role = new stdClass();
   $admin_role->name = 'administrator';
   user_role_save($admin_role);
-  user_role_set_permissions($admin_role->name, array_keys(module_invoke_all('permission')));
+  $admin_role_permissions = array();
+  foreach (array_keys(module_invoke_all('permission')) as $permission) {
+    $admin_role_permissions[$permission] = 1;
+  }
+  user_role_set_permissions($admin_role->name, $admin_role_permissions);
   // Set this as the administrator role.
   variable_set('user_admin_role', $admin_role->rid);
 
Index: profiles/expert/expert.install
===================================================================
RCS file: /cvs/drupal/drupal/profiles/expert/expert.install,v
retrieving revision 1.2
diff -u -p -r1.2 expert.install
--- profiles/expert/expert.install	27 Aug 2009 20:25:29 -0000	1.2
+++ profiles/expert/expert.install	10 Sep 2009 17:54:40 -0000
@@ -68,8 +68,8 @@ function expert_install() {
   $query->execute();  
 
   // Enable default permissions for system roles.
-  user_role_set_permissions(DRUPAL_ANONYMOUS_RID, array('access content'));
-  user_role_set_permissions(DRUPAL_AUTHENTICATED_RID, array('access content', 'access comments', 'post comments', 'post comments without approval'));
+  user_role_set_permissions(DRUPAL_ANONYMOUS_RID, array('access content' => 1));
+  user_role_set_permissions(DRUPAL_AUTHENTICATED_RID, array('access content' => 1, 'access comments' => 1, 'post comments' => 1, 'post comments without approval' => 1));
 }