It used to index everything! Now the site is not dynamic, it has a site map page, perhaps the only drawback is the use of js navigation.

Is it a new rule or something, to index only pages linked from the home page or there is something that could be done to change it?

www.translatum.gr

The JS menu is nav is your problem. check your site out in lynx viewer. if you can't see the links, google can't see the links
http://www.delorie.com/web/lynxview.html

Yes, I sort of suspected that that is why I have used many text links in the home page which also point to the site map page. Now the site map gets indexed but not the pages it points to (unless they also happen to have links from the home page).