diff --git src/bp-core/admin/bp-core-admin-components.php src/bp-core/admin/bp-core-admin-components.php
index ba868a8..434c152 100644
--- src/bp-core/admin/bp-core-admin-components.php
+++ src/bp-core/admin/bp-core-admin-components.php
@@ -299,7 +299,9 @@ function bp_core_admin_get_active_components_from_submitted_settings( $submitted
 		$current_action = $_GET['action'];
 	}
 
-	$current_components = buddypress()->active_components;
+	$current_components       = buddypress()->active_components;
+	$packaged_components      = array_flip( bp_core_get_packaged_component_ids() );
+	$custom_active_components = array_diff_key( $current_components, $packaged_components );
 
 	switch ( $current_action ) {
 		case 'retired' :
@@ -307,6 +309,11 @@ function bp_core_admin_get_active_components_from_submitted_settings( $submitted
 			foreach ( array_keys( $retired_components ) as $retired_component ) {
 				if ( ! isset( $submitted[ $retired_component ] ) ) {
 					unset( $current_components[ $retired_component ] );
+
+					// Make sure custom components does not contain a retired component
+					if ( isset( $custom_active_components[ $retired_component ] ) ) {
+						unset( $custom_active_components[ $retired_component ] );
+					}
 				}
 			}
 			// fall through
@@ -322,7 +329,8 @@ function bp_core_admin_get_active_components_from_submitted_settings( $submitted
 			break;
 	}
 
-	return $components;
+	// Active components is the list of packaged and custom components
+	return array_merge( $components, $custom_active_components );
 }
 
 /**