Bahasa Indonesia and Vietnamese were two languages I had SE subs for but could not convert, because the words were so numerous/big they couldn't always fit on two lines at a readable size. I suspect this could be an issue with any language that was retrofitted with a Latin alphabet to replace its native alphabet, so Bahasa Malaysia would fall into that category too. It's very similar to the issues faced in the Nordic subs, where literal line-for-line translation would result in word salad all over the screen.
With the help of a native speaker who could handle some trimming and paraphrasing, however, we could make it work. I'm hopeful.
EDIT: Actually those are the very Bahasa Indonesia SE subtitles I have! If he's willing to help us trim these down or retime them for the OOT, it would be awesome. I want to keep all languages to a maximum of two lines of text, three starts to have problems.