Problem with preserving subtitles when converting .mov file

[hypersapien]

Hello- I have tried to find the answer to this question by searching these forums, but I'm too much of a novice to know what terminology to search for in the first place. So I apologize if this has been answered before.

Basically, I am starting with a .mov video file which has subtitles in it and plays perfectly. I need to convert it to something iPad-friendly, but every method I have tried results in either a video with no subtitles, or a video with ONLY subtitles. I have tried using quicktime pro to export "to apple tv", and I have also used the Handbrake GUI and the following terminal prompt for handbrake:

1) Fire up Terminal (Inside utilities folder).
2) Type "cd " then drag the folder you want to process over the terminal window. The path should then be paste in. Hit return.
3) Paste the first line "for InputItem in *;" and hit return.
4) Paste the second line "do /Applications/HandBrakeCLI -i "$InputItem" -o "${InputItem}-Processed.mp4" --preset "Universal";" and hit return.
5) Type the third line "done" and hit return.
The handbrake CLI should then take over and process all the files, regardless of file type.

Some of the threads I've found regarding subtitles mention using MKVtools, which I have downloaded, but don't understand how to use.

So any help would be appreciated. I have converted dozens of .mov files with subtitles in the past with no problems, I just cant figure out what is different about this particular file...