The problem comes up with more than one 5.1 audio on the same audio track because obviously Encore is not able to join them like a dos command can do, poor and sad.
I am not quite sure what you are referring to here. Do you mean that you have several Audio Tracks (all DD 5.1 SS, but different versions) for each Encore Timeline, or something else?
It is usually not advised to gang several Video & Audio Clips onto a single Timeline, as problems can result, if that is what you mean.
Good luck,
Hunt