Did you remove the wrong audio tracks when using CloneDVD? Did you remove ANY audio tracks to save space? Some dvds have their audio tracks flagged incorrectly, and you may have removed the main audio track and left only the director's commentary...normally the director's commentary is only 2 channel, and the main feature audio tracks are 6 channel audio. You should really be posting this in a CloneDVD forum, though.
It really sounds like you removed the wrong audio track though...next time, right after CloneDVD does its job but BEFORE you burn, open the VIDEO TS folder and play the movie with your software dvd player, and see what audio tracks you can hear. This will let you hear what audio tracks are present before you create a coaster.