I have ripped the Lord Of The Rings extended edition to HD with magic DVD ripper, I have used main movie mode (copy main movie) with some audio and some subtitles. Then as usual AutoGknot to convert to xvid.
AutoGknot ignored one of the subtitls (czech) and included only the english ones. I have tried with vobsub to extract the subtitles, it extracted both of them but only english ones show on the screen. Playing the movie from the ripped files (on HD) with media player classic shows both english and czech subtitles. I have already more than 100 films in xvid and this is the first time I faced a problem. What I'm doing wrong?

Thanks in advance.