Recently one of my sites was upgraded to Drupal 5.7 from 5.1 and I was get a 404 or page not found error on all pages of my website except the front page. How I solved this.

1. I ran update.php again. This fixed my navigation. But clean urls were not working.
2. I found that .htaccess was corrupted. I transfered it again. bingo! it worked.
3. Finally I enabled clean URLS from my admin panel.

For more information on this error visit http://drupal.org/node/262892

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Thanks