For DVD you would normally use elementary streams, not multiplexed streams. But to play back with a software player on a computer, you need a multiplexed stream and since you have elementary streams, there is no sound from the software player.
So I should just burn to DVD using Encore, and they should be all right?
They should be just fine, and work perfectly in Encore.
Now, if there was a situation, where you needed both Streams in one file, what you would do is go to the Multiplexer Tab in the AME settings, and choose DVD (most common, though it does differ for some Export formats), in lieu of None. This ARTICLE goes into more detail on Multiplexing.