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Up to version 2.1.1, SEOGlossary, from Joomunited, as a small bug which, when SEOGLossary is used together with RocketTheme templates (more precisely the mod_roknavmenu menu module) will cause sh404SEF to create menu links going to the home page.

The temporary fix is to modify this SEO Glossary file: /plugins/content/seoglossary/seoglossary.php.

The exact line number depends on your SEO Glossary version, it's line 91 for SEOG version 2.1. In any case, you should locate the code:

$menu->link = JRoute::_($menu->link);
$furl = $_SERVER['REQUEST_URI'];
if (strcmp($furl, html_entity_decode($menu->link)) == 0)

and replace it with:

$menuLink = JRoute::_($menu->link);
$furl = $_SERVER['REQUEST_URI'];
if (strcmp($furl, html_entity_decode($menuLink)) == 0)

An upcoming version should fix the problem in SEOGlossary.