Bob,
My suspicion is that some of the audio you have used is in MPEG-1 Layer II (mpa) format, instead of Dolby Digital (AC3) or PCM (wav). NTSC set top DVD players are not required to support MPEG audio and even if a player does, then this type of audio will only be sent to the analog output and not to the digital one.
Preferably all audio imported in Encore should be PCM, 48KHz, 16 bit, stereo and be transcoded by Encore to Dolby Digital. (Or imported as Dolby Digital.) If there is no other source available than the MPEG-1 Layer II audio, make sure that you let Encore convert it to AC3.