Like I said before, I had doubts about Crunchyroll’s multi-audio capabilities, because Crunchyroll has separate videos for each audio, and quite a few titles (the ones released before the merge) have different lengths when it comes to multi-language (due to different logo openings, especially the ones from Funimation. A lot have Crunchy opening for sub and Funni opening for dub, resulting in different video lengths). I have encountered once what you described, with an old title that have different sub and dub, and only Japanese audio was downloaded despite both checking both options. But when i download a newer title that has both language with the same length, it downloaded as it should, with both audios intact. So check the videos for the openings of each language, if different, you probably have to do it like the old way–download each audio separately.
