Index: wp-admin/plugins.php
===================================================================
--- wp-admin/plugins.php	(revision 6713)
+++ wp-admin/plugins.php	(working copy)
@@ -92,6 +92,10 @@
 	</thead>
 <?php
 	$style = '';
+	
+	foreach($current_plugins as $plugin_file) //Check that all the active plugins are on the plugins list.
+		if ( empty($plugins) || ! isset( $plugins[ $plugin_file] ) )
+			deactivate_plugins($plugin_file);
 
 	foreach($plugins as $plugin_file => $plugin_data) {
 		$style = ('class="alternate"' == $style|| 'class="alternate active"' == $style) ? '' : 'alternate';