duplicate entries

I was trying to enable aggregator in drupal 6.14 then nothing was showing. When I tried to run cron, I had some errors. lots of them. I tried to run update then I had a lot of duplicate entries on menu.inc, on line 2423. I checked the code but it's not something that I understand. I tried to isolate the offending code. Here:
// Calculate out the file to be included for each callback, if any.
if ($item['file']) {
$file_path = $item['file path'] ? $item['file path'] : drupal_get_path('module', $item['module']);
$item['include file'] = $file_path .'/'. $item['file'];
}

$title_arguments = $item['title arguments'] ? serialize($item['title arguments']) : '';
db_query("INSERT INTO {menu_router} SELECT DISTINCT
(path, load_functions, to_arg_functions, access_callback,
access_arguments, page_callback, page_arguments, fit,
number_parts, tab_parent, tab_root,
title, title_callback, title_arguments,
type, block_callback, description, position, weight, file)
VALUES ('%s', '%s', '%s', '%s',
'%s', '%s', '%s', %d,
%d, '%s', '%s',
'%s', '%s', '%s',
%d, '%s', '%s', '%s', %d, '%s')",
$path, $item['load_functions'], $item['to_arg_functions'], $item['access callback'],
serialize($item['access arguments']), $item['page callback'], serialize($item['page arguments']), $item['_fit'],
$item['_number_parts'], $item['tab_parent'], $item['tab_root'],
$item['title'], $item['title callback'], $title_arguments,
$item['type'], $item['block callback'], $item['description'], $item['position'], $item['weight'], $item['include file']);
Then I restored the database to an earlier version, hoping to get rid of the issue, if it were related to something that I may have introduced later in the phase. Now I'm getting this error:
Duplicate entry 'sites/all/themes/theme041/theme041.info' for key 1 query: INSERT INTO drup_system (name, owner, info, type, filename, status, throttle, bootstrap) VALUES ('theme041', 'themes/engines/phptemplate/phptemplate.engine', 'a:13:{s:4:\"name\";s:8:\"theme041\";s:11:\"description\";s:43:\"this template is made by template-help.com.\";s:7:\"version\";s:3:\"6.2\";s:4:\"core\";s:3:\"6.x\";s:6:\"engine\";s:11:\"phptemplate\";s:7:\"project\";s:6:\"drupal\";s:9:\"datestamp\";s:10:\"1202913006\";s:3:\"php\";s:5:\"4.3.5\";s:7:\"regions\";a:6:{s:6:\"header\";s:6:\"Header\";s:4:\"left\";s:12:\"Left sidebar\";s:5:\"right\";s:13:\"Right sidebar\";s:7:\"content\";s:7:\"content\";s:6:\"footer\";s:6:\"Footer\";s:7:\"welcome\";s:7:\"Welcome\";}s:8:\"features\";a:10:{i:0;s:20:\"comment_user_picture\";i:1;s:7:\"favicon\";i:2;s:7:\"mission\";i:3;s:4:\"logo\";i:4;s:4:\"name\";i:5;s:17:\"node_user_picture\";i:6;s:6:\"search\";i:7;s:6:\"slogan\";i:8;s:13:\"primary_links\";i:9;s:15:\"secondary_links\";}s:11:\"stylesheets\";a:1:{s:3:\"all\";a:1:{s:9:\"style.css\";s:35:\"sites/all/themes/theme041/style.css\";}}s:7:\"scripts\";a:1:{s:9:\"script.js\";s:35:\"sites/all/themes/theme041/script.js\";}s:10:\"screenshot\";s:40:\"sites/all/themes/theme041/screenshot.png\";}', 'theme', 'sites/all/themes/theme041/theme041.info', 1, 0, 0) in /home/givepacc/public_html/modules/system/system.module on line 822.
If I disable Aggregator, the error is gone, but still cron fails to run.
Any help will be appreciated.