Mp4 and subtitles

Hi

I have this Lord of the rings DVD. I converted 1st and second movie to mp4 using nero recode 2 including subtitles. I choose the option of split in 3 CD 80 mins.

My problem is that when I play the movie in showtime, in the 1st CD it shows perfectly subtitles. but in the 2nd and the 3rd of the movies I have a problem with subtitles. they are a little anticipated. In the beginning subtitles of the next starting chapter are shown.

Does it has any solution during playback, how does this can be avoided during movie encode?

Thanks in advance

Harold