diff --git wp-admin/includes/class-wp-upgrader.php wp-admin/includes/class-wp-upgrader.php
index ef8fb5f..94afe34 100644
--- wp-admin/includes/class-wp-upgrader.php
+++ wp-admin/includes/class-wp-upgrader.php
@@ -580,11 +580,24 @@ class Plugin_Upgrader extends WP_Upgrader {
 		if ( empty($plugin) )
 			return false;
 
-		$pluginfiles = array_keys($plugin); //Assume the requested plugin is the first in the list
+		$pluginfiles = array_keys($plugin);
+
+		usort( $pluginfiles, array( $this, '_plugin_info_sort_comparison' ) );
 
 		return $this->result['destination_name'] . '/' . $pluginfiles[0];
 	}
 
+	/**
+	 * Internal function for comparing paths to sort plugin files in no directory to the top.
+	 * 
+	 * @param  string $plugin_file_a
+	 * @param  string $plugin_file_b
+	 * @return int
+	 */
+	function _plugin_info_sort_comparison( $plugin_file_a, $plugin_file_b ) {
+		return strstr( $plugin_file_a, '/' ) ? 1 : -1;
+	}
+
 	//Hooked to pre_install
 	function deactivate_plugin_before_upgrade($return, $plugin) {