Let's take DVD Shrink for an example.... when selecting what to back up, you can either select or deselect subtitles. It's during playback however, that you either through the players settings OR the Audio settings of the actual movie, that these are enabled. It's my experience that subtitles don't automatically "engage" during playback.
If your having further problems with your backups, tell us what software you use so we can assist you better. To FORCE subtitles to play automatically, is outside my limited expertise. Stay tuned just in case a member has an answer.
If your DVD is 'Movie only' (or you don't mind making it so) you can use DVDShrink. Open it and hit Reauthor, then Right click-> Set Default Streams and choose your subs. Resave 'Uncompressed' and you'll be good to go.
