I had Legacy mode turned on because an earlier version required it when I created this website. I've since updated and am now in 3.9.2. When I turn off Legacy mode, all the links do not work at all, meaning, if I'm on a page and select a menu item, it won't send me there. It keeps me on the same page. Turn back on Legacy and it works. This happens with menu links and on page links. The url shows the SEF url, but it's wrong. I don't go anywhere.

I'm assuming this is a problem with JoomSEF and not Joomla. Or am I wrong? How do I fix this?