What happened is this, as far as I can tell.
Simoni(sp?) had said that a friend and former doctor of Armstrongs and Semoni, Ferrari, prescribed steroid like drugs to cyclists. Armstrong said that such flase claims are 'ruining' the sport, not to mention casting light on Armstrong's achievements. So, Armstrong decided to ride next to Simoni the whole way to make sure we did not win the stage. When Simoni (and armstrong) caught up to the lead bunch, they told Simoni to get away, cause Armstrong was tagging along, and he would win the stage. So Simoni dropped back (because of this, Armstrong did too), and the group up in front could race against each other, not Armstrong.
Kind of odd, imo, but Armstrong is still up by something like 4:09, so he could afford to do it I guess.