@mojonek, @schwipps - We cannot really reproduce your problem. For a term description permalink we rely on WordPress core mechanism (slug for custom post type). Could you provide some address where we can check and debug that issue? Could you also check if changing 'with_front' to true on glossary.php line 70 and if saving permalinks (settings->permalinks) changes anything?
@hrdo2001 - Parent index is actually a static page with the title and permalink as specified on "Pages" panel. So term pages are in fact independent from that index and have separate structure. To tell you what you can do to alter breadcrumbs display on term page, you would need to send us what do you use for generating breadcrumbs - is it some plugin or is it in theme? If so, what is its name?