Unfortunately, I haven't found a solution for this either.
As I understand it, this happens when they have a single English subtitle track on the disc, but only play parts of it by default for the non-English sections, displaying the full thing if you actually enable subtitles when watching the film.
I don't think MakeMKV has anything in it to detect this yet, and I've kept those discs as .iso until someone figures out a way to rip them properly.
Another thing I've run into on a couple of Blu-ray discs recently is that they have a lot of subtitle tracks beyond the standard English and English SDH/CC.
So far, I haven't been able to figure out what the additional tracks are for (short of watching the whole film) and as far as I recall, the films only had English spoken in them, and they did not have a commentary track. From scanning through a few sections on the disc, they seem to be the same as the regular English track. ?
It's the one thing about using an HTPC that I wish was easier. If you rip to ISO, you retain everything, but you also waste 10GB+ per disc most of the time - less with DVDs, but then you have menus to deal with.