diff --git a/includes/mail.inc b/includes/mail.inc
index 7dd2860..71ea19c 100644
--- a/includes/mail.inc
+++ b/includes/mail.inc
@@ -285,7 +285,7 @@ function project_issue_mail_notify($nid) {
   // 'Own' level using the list of users attached to the issue.
   if (!empty($own_issues_uids)) {
     $placeholders = implode(',', array_fill(0, count($own_issues_uids), '%d'));
-    $filter_array[] = "(pi.uid IN ($placeholders) AND pi.level = " . PROJECT_ISSUE_SUBSCRIPTIONS_FLAGGED . ")";
+    $filter_array[] = "(pi.level = " . PROJECT_ISSUE_SUBSCRIPTIONS_FLAGGED . " AND u.uid IN ($placeholders))";
     $args = array_merge($args, $own_issues_uids);
   }
   $filter = implode(" OR ", $filter_array);
diff --git a/project_issue.install b/project_issue.install
index f4e8fa1..3e4ad08 100644
--- a/project_issue.install
+++ b/project_issue.install
@@ -303,7 +303,7 @@ function project_issue_schema() {
     ),
     'primary key' => array('uid'),
     'indexes' => array(
-      'uid_level' => array('uid', 'level'),
+      'level' => array('level'),
     ),
   );
 
@@ -335,7 +335,7 @@ function project_issue_schema() {
     ),
     'primary key' => array('uid', 'nid'),
     'indexes' => array(
-      'project_subscriptions_nid_uid_level' => array('nid', 'uid', 'level'),
+      'nid_level' => array('nid', 'level'),
     ),
   );
 
@@ -654,9 +654,18 @@ function project_issue_update_6006() {
 }
 
 /**
+ * Ensure that existing project subscriptions are clean.
+ */
+function project_issue_update_6007() {
+  $ret = array();
+  $ret[] = update_sql("DELETE FROM {project_subscriptions} WHERE level = 0");
+  return $ret;
+}
+
+/**
  * Clean up duplicates in {project_subscriptions}.
  */
-function project_issue_update_6007(&$sandbox) {
+function project_issue_update_6008(&$sandbox) {
   $ret = array();
 
   if (!isset($sandbox['total'])) {
@@ -693,9 +702,10 @@ function project_issue_update_6007(&$sandbox) {
 }
 
 /**
- * Revamp project issue subscriptions for Flag integration.
+ * Move subscriptions into the project_issue namespace, and split into
+ * user-level and project-level.
  */
-function project_issue_update_6008() {
+function project_issue_update_6009() {
   $ret = array();
 
   // Delete obsolete 'project_issue_global_subscribe_page' variable.
@@ -726,7 +736,7 @@ function project_issue_update_6008() {
     ),
     'primary key' => array('uid'),
     'indexes' => array(
-      'uid_level' => array('uid', 'level'),
+      'level' => array('level'),
     ),
   ));
 
@@ -734,23 +744,37 @@ function project_issue_update_6008() {
 }
 
 /**
- * Ensure that existing project subscriptions are clean.
+ * Add primary key to {project_issue_subscriptions_project}.
+ *
+ * WARNING: This update can take a *very* long time (potentially hours) if
+ * there are a high number of rows in the table. The test table had 2.34
+ * million rows, and the query took over three hours on reasonable hardware.
  */
-function project_issue_update_6009() {
+function project_issue_update_6010() {
   $ret = array();
-  $ret[] = update_sql("DELETE FROM {project_issue_subscriptions_project} WHERE level = 0");
+  db_add_primary_key($ret, 'project_issue_subscriptions_project', array('uid', 'nid'));
   return $ret;
 }
 
 /**
- * Add primary key to {project_issue_subscriptions_project}.
+ * Add nid_level key to {project_issue_subscriptions_project}.
  *
  * WARNING: This update can take a *very* long time (potentially hours) if
- * there are a high number of rows in the table. The test table had 2.34
- * million rows, and the query took over three hours on reasonable hardware.
+ * there are a high number of rows in the table.
  */
-function project_issue_update_6010() {
+function project_issue_update_6011() {
   $ret = array();
-  db_add_primary_key($ret, 'project_issue_subscriptions_project', array('uid', 'nid'));
+  db_add_index($ret, 'project_issue_subscriptions_project', 'nid_level', array('nid', 'level'));
   return $ret;
 }
+
+/**
+ * Drop unneccessary indexes from {project_issue_subscriptions_project}.
+ */
+function project_issue_update_6012() {
+  $ret = array();
+  db_drop_index($ret, 'project_issue_subscriptions_project', 'uid');
+  db_drop_index($ret, 'project_issue_subscriptions_project', 'project_subscriptions_nid_uid_level');
+  return $ret;
+}
+
diff --git a/project_issue.module b/project_issue.module
index 06f552d..a261bd6 100644
--- a/project_issue.module
+++ b/project_issue.module
@@ -949,28 +949,19 @@ function project_issue_subscriptions_user_settings_load($account) {
  *       - PROJECT_ISSUE_SUBSCRIPTIONS_NONE
  *       - PROJECT_ISSUE_SUBSCRIPTIONS_FLAGGED
  *       - PROJECT_ISSUE_SUBSCRIPTIONS_ALL
- *     When passing PROJECT_ISSUE_SUBSCRIPTIONS_NONE the user's per-user
- *     subscription setting is deleted.
  *
  * @see project_issue_subscriptions_user_settings_load()
  */
 function project_issue_subscriptions_user_settings_save($account) {
   $level = $account->project_issue_subscriptions['level'];
-  if ($level > PROJECT_ISSUE_SUBSCRIPTIONS_NONE) {
-    db_query("UPDATE {project_issue_subscriptions_user} SET level = %d WHERE uid = %d", array(
-      $level,
-      $account->uid,
-    ));
-    if (!db_affected_rows()) {
-      db_query("INSERT INTO {project_issue_subscriptions_user} (uid, level) VALUES (%d, %d)", array(
-        $account->uid,
-        $level,
-      ));
-    }
-  }
-  else {
-    db_query("DELETE FROM {project_issue_subscriptions_user} WHERE uid = %d", array(
+  db_query("UPDATE {project_issue_subscriptions_user} SET level = %d WHERE uid = %d", array(
+    $level,
+    $account->uid,
+  ));
+  if (!db_affected_rows()) {
+    db_query("INSERT INTO {project_issue_subscriptions_user} (uid, level) VALUES (%d, %d)", array(
       $account->uid,
+      $level,
     ));
   }
 }