did you turn on subtitles in the menu?
have you tried the "subtitle" button on your dvd player's remote control.
if neither of these options work then it seems you've failed to include the english subtitles on your backup. I'd re-rip the disc and pay closer attention to what you've selected in regards to subtitles.
also you didn't state the version of clonedvd that you're using. an older version failed to include anything that was selected via the left hand pane in the audio selection window, but would include it if you selected the audio/subtitle streams under the stream preferences in the right hand pane.
the latest version of clonedvd2 (184.108.40.206) does away with this small bug.