After installing the newest version of JoomSEF, I cannot open any of my sites pages.

My Joomla site is located in a subdirectory. When version 1.5.1 was installed, everything worked fine. After upgrading to 2.0.2, opening a page results in a 404 error page (the 404 of page of JoomSEF). The error on top of the page says (where v5/cms is the subdirectory in which my site is installed).

I took a look a the control panel, but could not find an option that forces a prefix on the pages or something. The pages in the list where filled like they were in the previous version. I reverted to version 1.5.1 and after that the problem was solved. I reinstalled version 2.0.2 and the problem reocurred.

Is there any solution to this problem?