The default extension provided by Xmap the popular site map tool for Joomla, does not always create correct links to articles for example:

An incorrect link is created when using the default Sectionex extension 1.0 for xmap 1.2.
http://www.weightcontrolsoftware.com/component/content/12-efit-manual-for-version-11.html

The correct link should be:
http://www.weightcontrolsoftware.com/guides/9-efitguide/12-efit-manual-for-version-11.html

The this is visible when SEF turned on. I have created a SectionEx extension based on the default one supplied with Xmap, that will work with SEF turned on.

I have not tested with SEF turned off, but it shouldn't take much to get it working for that too. My extension creates the same url as created by SectionEx and therefore is better for SEO (Search Engine Optimization) as XMAP no longer creates different urls to the same page.

Download: SectionEx Xmap extension