Problems with Copy of live site prior upgrading

[icecold]

I created a copy of my site in another directory and modified the configuration files accordingly, not upload anything from 1.3.9h yet, just my custom 1.3.8a, within a new directory named a2, while the live site resides under a, so they are www.domain.com/a the live one, and www.domain.com/a2 the test copy.

I made a copy of the db, and modified both configuration files, and checked the changes are there, so the site correctly points to a2 instead of a, and the new database(this connection works fine, albeit was slow).

So the home page under a2 works fine, and displays the products and everything as it supposes to, but and here is the weir thing if I select a category, and click it shows a 'Page not found' error, and the path looks like this http://www.domain.com/a/a2/name-of-the-category, as I am using Simple SEO ...

To test this for real please follow this link to the live store http://www.theoutletseason.com/electronics and to visit the test site simply add '2' at the end of electronics.