Convert MKV to iPod MP4

Recently, I decided to use my backup Win Vista Home Basic's iTunes to load anime I have into my iPod. Most anime are served out in MKV H264 format and I used KigoConverter to convert MKV to Custom MP4 (iPod uses this). What I noticed is that by doing so, the scipts containing the english translations are omitted and I am left to listen and watch the animes on my iPod without any translations and this can be hard on those who have no idea about Japanese language.

I noticed that AVI videos when converted to MP4 have their translations retained and you can watch them properly.... hmmm... I am wondering why did the translations scripts not be added to the custom MP4. Does anyone have any answers ?