If any menu items go missing from the Administrator side of things, try running the following sql.

Original menu items for a base Joomla 3.3.x install.

INSERT IGNORE INTO `prefix_menu` (`id`, `menutype`, `title`, `alias`, `note`, `path`, `link`, `type`, `published`, `parent_id`, `level`, `component_id`, `checked_out`, `checked_out_time`, `browserNav`, `access`, `img`, `template_style_id`, `params`, `lft`, `rgt`, `home`, `language`, `client_id`) VALUES
(1, '', 'Menu_Item_Root', 'root', '', '', '', '', 1, 0, 0, 0, 0, '0000-00-00 00:00:00', 0, 0, '', 0, '', 0, 327, 0, '*', 0),
(2, 'menu', 'com_banners', 'Banners', '', 'Banners', 'index.php?option=com_banners', 'component', 0, 1, 1, 4, 0, '0000-00-00 00:00:00', 0, 0, 'class:banners', 0, '', 5, 14, 0, '*', 1),
(3, 'menu', 'com_banners', 'Banners', '', 'Banners/Banners', 'index.php?option=com_banners', 'component', 0, 2, 2, 4, 0, '0000-00-00 00:00:00', 0, 0, 'class:banners', 0, '', 6, 7, 0, '*', 1),
(4, 'menu', 'com_banners_categories', 'Categories', '', 'Banners/Categories', 'index.php?option=com_categories&extension=com_banners', 'component', 0, 2, 2, 6, 0, '0000-00-00 00:00:00', 0, 0, 'class:banners-cat', 0, '', 8, 9, 0, '*', 1),
(5, 'menu', 'com_banners_clients', 'Clients', '', 'Banners/Clients', 'index.php?option=com_banners&view=clients', 'component', 0, 2, 2, 4, 0, '0000-00-00 00:00:00', 0, 0, 'class:banners-clients', 0, '', 10, 11, 0, '*', 1),
(6, 'menu', 'com_banners_tracks', 'Tracks', '', 'Banners/Tracks', 'index.php?option=com_banners&view=tracks', 'component', 0, 2, 2, 4, 0, '0000-00-00 00:00:00', 0, 0, 'class:banners-tracks', 0, '', 12, 13, 0, '*', 1),
(7, 'menu', 'com_contact', 'Contacts', '', 'Contacts', 'index.php?option=com_contact', 'component', 0, 1, 1, 8, 0, '0000-00-00 00:00:00', 0, 0, 'class:contact', 0, '', 15, 20, 0, '*', 1),
(8, 'menu', 'com_contact', 'Contacts', '', 'Contacts/Contacts', 'index.php?option=com_contact', 'component', 0, 7, 2, 8, 0, '0000-00-00 00:00:00', 0, 0, 'class:contact', 0, '', 16, 17, 0, '*', 1),
(9, 'menu', 'com_contact_categories', 'Categories', '', 'Contacts/Categories', 'index.php?option=com_categories&extension=com_contact', 'component', 0, 7, 2, 6, 0, '0000-00-00 00:00:00', 0, 0, 'class:contact-cat', 0, '', 18, 19, 0, '*', 1),
(10, 'menu', 'com_messages', 'Messaging', '', 'Messaging', 'index.php?option=com_messages', 'component', 0, 1, 1, 15, 0, '0000-00-00 00:00:00', 0, 0, 'class:messages', 0, '', 21, 26, 0, '*', 1),
(11, 'menu', 'com_messages_add', 'New Private Message', '', 'Messaging/New Private Message', 'index.php?option=com_messages&task=message.add', 'component', 0, 10, 2, 15, 0, '0000-00-00 00:00:00', 0, 0, 'class:messages-add', 0, '', 22, 23, 0, '*', 1),
(12, 'menu', 'com_messages_read', 'Read Private Message', '', 'Messaging/Read Private Message', 'index.php?option=com_messages', 'component', 0, 10, 2, 15, 0, '0000-00-00 00:00:00', 0, 0, 'class:messages-read', 0, '', 24, 25, 0, '*', 1),
(13, 'menu', 'com_newsfeeds', 'News Feeds', '', 'News Feeds', 'index.php?option=com_newsfeeds', 'component', 0, 1, 1, 17, 0, '0000-00-00 00:00:00', 0, 0, 'class:newsfeeds', 0, '', 27, 32, 0, '*', 1),
(14, 'menu', 'com_newsfeeds_feeds', 'Feeds', '', 'News Feeds/Feeds', 'index.php?option=com_newsfeeds', 'component', 0, 13, 2, 17, 0, '0000-00-00 00:00:00', 0, 0, 'class:newsfeeds', 0, '', 28, 29, 0, '*', 1),
(15, 'menu', 'com_newsfeeds_categories', 'Categories', '', 'News Feeds/Categories', 'index.php?option=com_categories&extension=com_newsfeeds', 'component', 0, 13, 2, 6, 0, '0000-00-00 00:00:00', 0, 0, 'class:newsfeeds-cat', 0, '', 30, 31, 0, '*', 1),
(16, 'menu', 'com_redirect', 'Redirect', '', 'Redirect', 'index.php?option=com_redirect', 'component', 0, 1, 1, 24, 0, '0000-00-00 00:00:00', 0, 0, 'class:redirect', 0, '', 47, 48, 0, '*', 1),
(17, 'menu', 'com_search', 'Basic Search', '', 'Basic Search', 'index.php?option=com_search', 'component', 0, 1, 1, 19, 0, '0000-00-00 00:00:00', 0, 0, 'class:search', 0, '', 37, 38, 0, '*', 1),
(18, 'menu', 'com_weblinks', 'Weblinks', '', 'Weblinks', 'index.php?option=com_weblinks', 'component', 0, 1, 1, 21, 0, '0000-00-00 00:00:00', 0, 0, 'class:weblinks', 0, '', 41, 46, 0, '*', 1),
(19, 'menu', 'com_weblinks_links', 'Links', '', 'Weblinks/Links', 'index.php?option=com_weblinks', 'component', 0, 18, 2, 21, 0, '0000-00-00 00:00:00', 0, 0, 'class:weblinks', 0, '', 42, 43, 0, '*', 1),
(20, 'menu', 'com_weblinks_categories', 'Categories', '', 'Weblinks/Categories', 'index.php?option=com_categories&extension=com_weblinks', 'component', 0, 18, 2, 6, 0, '0000-00-00 00:00:00', 0, 0, 'class:weblinks-cat', 0, '', 44, 45, 0, '*', 1),
(21, 'menu', 'com_finder', 'Smart Search', '', 'Smart Search', 'index.php?option=com_finder', 'component', 0, 1, 1, 27, 0, '0000-00-00 00:00:00', 0, 0, 'class:finder', 0, '', 33, 34, 0, '*', 1),
(22, 'menu', 'com_joomlaupdate', 'Joomla! Update', '', 'Joomla! Update', 'index.php?option=com_joomlaupdate', 'component', 0, 1, 1, 28, 0, '0000-00-00 00:00:00', 0, 0, 'class:joomlaupdate', 0, '', 35, 36, 0, '*', 1);