Website not working after update to 7.26

I had running Drupal 7.22 or 7.23 and this website worked fine.

I received mail that I should update to a newer version and yesterday the latest stable version was 7.26

I downloaded & unpacked it. After that, I replaced the old files with the new one. The files/directories that came not with the update stayed on the server.

This is the problem: If I go the website, the first webpage is shown. But when I click on a link to go to the next page, I get a 404 error. If I wants to go to the administration dashboard, I get a 404 error.

When I run update.php I get the following message : No pending updates.
I rebuilded the node permissions.

But when I use this: "http://www.yoursite.com/?q=........." and put on the ..... the right address, the requested page is available.

My question is : What is going wrong ?

Thanks in advance for your help !