Can't see my website's pages, except the Homepage

I have a problem with nav menu links not working, or maybe it’s the pretty-url, or maybe else. Need help to fix this one 🙂

I made a site in 2010, using a child theme for TwentyTen at the time. Never updated this site since.

When I installed the site it was 3.0.2
My dashboard says : You are using WordPress 3.1.3. (please update to 3.9.2)

When I visit it toady, I tried clicking the main nav menu link, but there was just no action at all on these links. So…

– I can see the other pages does exist and are Published in Admin… but when i click See Page from the admin it sends me to mysite.com/pagename but it’s home (homepage, but showing the page url)

– When I put my mouse over the nav menu, I still see the old links url down-bottom of my browser (http://mysite.com/?page_ID=123), even tough I have carefully selected Custom /%postname% in Settings > Permalinks

– I have also made sure I have a .htaccess file

– I dont use any Plugins at all

– My header.php file use exact same code as the main theme file, for the nav menu section

– Everything looks perfect on the only page I can see, the homepage (colors, layout, logo, etc)

Help please!