update to 2.4.0 or 2.4.1 breaks permalinks of custom taxonomies

hi jonathan

i have a multilanguage site (using WPML, 2 languages) with a custom post type and a few related custom taxonomies.

i have an archive template that handles these taxonomies, and clicking on terms on a custom menu brings up the correct results, even with multiple terms:

domain.ext/section/taxonomy1/termoftax1/taxonomy2/termoftax2

this would bring up a page of all posts of the custom post type that match termoftax1 and termoftax2.

in the menu, i also have a widget for BTF. up to version 2.3.5 the conditional function wasn’t working at all, but selecting multiple terms from different pulldown menus would work as above.

now, i tried version 2.4.0 on a clone of the site: right after activating it, the links on the custom menu would produce only 404s. same happened using the BTF widget, so i trashed the clone and reverted to version 2.3.5: all went back to working (apart from the conditional function, of course).

the next day i saw 2.4.1 coming and your note about rewrite rules. i tested it on the clone, and the same things happened: conditional was working, but applying the filter would end up in 404, as well as the custom menu links, as happened with version 2.4.0.

could you help me out with the problem?