Neti,
What I had to do was rename that sef_ext file,purge all SEF URLs in the Artio admin page, then immediately load my site from the root URL
www.yoursitename.com. Then I clicked on all of the main menu links. Then I checked and all of my links were working from my MTree directory pages as well as my Most Popular module links.
Try that. I think if you clear the SEF URLs and then try to reload any page other than the main root URL for your site, it screws up the paths that JoomSEF maps.
Good luck!