I'm trying to eliminate possible errors as we go. The straight rip should play with subtitles available throughout. If you play this straight rip, you should be able to confirm this by playing in one of the media players I've suggested, though Windows Media Player in Win 7 does have dvd capability as well if you'd prefer to use it.
We generally recommend other players because they are known quantities to us, and we understand the way they work. That helps us diagnose issues on occasion, and sometimes we just like to show that there are other options available.
Some dvds are more difficult to decrypt than others. Slysoft recommends ripping these difficult ones to the hard drive first, before trying to process them, or convert them to other formats.
The loss of part of the subtitles is a bit strange though. This is not a normal problem.
Since I am not familiar with the CloneDVD Mobile program, I probably won't be of much help with it. I can offer you alternative programs that are free to use if you want to try them with these particular, problem dvds. First step is to rip the entire thing to the hard drive. Then use either Vidcoder or Handbrake to convert to formats that will work in your Apple TV or iPad. Both of these programs have presets for those devices.