lisaleague on "[Plugin: WordPress SEO by Yoast] Categories & Sitemap return 404 errors"

WordPress version: 3.4.1
WordPress SEO version: 1.2.5
I did this: installed and have kept up to date
I expected the plugin to do this: create xml site map
Instead it did this:

All categories and tags now return 404 errors
The XML sitemap now returns a 404 error

For example category "NCIDQ Section 2" slug is ncidq-section-2 & url is

http://www.qpractice.com/ncidq-section-2/ but returns a 404

NCIDQ Section 1 slug is ncidq-section-1 but returns a 404
NCIDQ Section 3 slug is ncidq-section-3 but returns a 404
Category NCIDQ Exam Study study slug is ncidq-exam-study
but returns http://www.qpractice.com/ncidq-exam-study-guide/

This problem is not just from the front end, but also when trying to view the category from the back and is regardless of whether I have these settings checked or unchecked.

http://wordpress.org/extend/plugins/wordpress-seo/