Who knows what the story is? He could be really ill. He did the Giro and the Dauphine which doesn't excuse his pitiful Tour performance but it goes some way to justifying it. His job was to escort Sastre and Schleck and it was clear he was not in form to do that.
Zabriskie is a tough dude -- all top time trial riders are. In the next couple of days we'll probably have a more cogent answer than some of the stuff being conjectured here and elsewhere.