I wonder if it make a difference to use
http://www.domain.com/category_base/category/ when you are using the
http://www.domain.com/%category%/%postname%/ method. Since you are using the base, is it still confused between /category/post and /category_base/category/.
Because the base is used, seems like the page and post urls will be easier to separate. I hope so at least, because thats how I have quite a few blogs set up lol.