I had the same problem with permalink but using standard WP menù pointing to GD category taxonomy. I really don’t understand the reason of doing that on permalinks (appending locations from previously visited places) since it gets pretty weird results and break some pages.
Anyways my solution was this:
remove_filter(‘term_link’, ‘geodir_get_term_link’);
Searching the code there’s one more hook that seems to be doing something with menù permalink, for me the first one was enought tho.
remove_filter( ‘term_link’, ‘geodir_cpt_term_link’, 9999);
I don’t knkow yet if this brings any other problem behind but ATM everything looks working great. I have the nice SEO friendly URL when clicking on place detail and i have the normal-looking URL when clicking back on another category from the main menù