The same exact thing has happened to me. My site is at
cbj.contendia.net . I uploaded the quickstart zip file to the public_html directory, used SSH to unzip it, then go through the installation wizard in the browser to setup the site. Everything worked fine. But now, none of the menu links work at all.
I have played around with some of the links and changed them, and when I do, I get the same long URL like:
/index.php/2013-05-13-12-50-59/module-positions