This indicates to me that you are not making your track selections in the "Preferences" area. You should make all your selections in the right hand pane.
To expand on this, when you are making audio and subtitle selections in CloneDVD, make all your choices ALL on the right hand pane entitled "Steam Preferences". Don't even click at all in the left hand pane entitled "Stream Configuration". Although the left pane is also user-interactive, think of it more as a confirmation of your right pane selections. Clicking around in there has, in the past, lead to some track functionality issues. Although the issue is supposed to have been resolved, per James.
I don't think you have to copy the whole DVD and all tracks ... movie only is ok, if that is your preferred method. just be sure you "Preserve Menus"