tags in post are now showing up as /taxonomy/term/1 instead of clean urls ???

Before i updated to this new version. I was able to show all post from sub categories in the root category. Now that does not work so each time a user click on the top level category menu it just says no content. How can i make it so that the top level category can show all sub categories?

Also, before it was taxonomy_menu/term/1 and now category/1 for menu links which is an improvement, thank you. But it seem to have reversed the process, my tags in post are now showing up as taxonomy_menu/term/1 instead of it's clean urls? I'm using Pathauto module as well if that might be an issue.

I hope i've explained it well, it's a difficut matter to make it clear.