Sites created with batch create have the categories from blogs templates, but they don't work

So I create sites with batch create and new blogs template. The categories in the blog template are in the sites created by batch create, but when you post using the categories on the newly created sites, and then click the categories on the widget or at the bottom of the post, I get page not found. If I remove the default blog template and try again with just the uncategorized category, it still doesn't work.

If I create a site manually, it still doesn't, whats going on?

It did work before I added the plugins! Any ideas?