I think that the fact that he lost something like a minute twentyone on the peloton in the last few kilometres probably should go to answer a few questions.
A one off break like that is probably the best way to look at it - a one off break by a good TT rider who was able to employ those skills in the last thirty Ks. It was chance that it turned up on the first week and was (is) still in contention for the Maillot Jaune; if anything, the fact that he was still in contention probably ruined his chances of taking the victory. Similarly, Voeckler's win yesterday was followed up by the expectable 151st of 177, 6m55 down. Whatever about anything else, it is unlikely he is on EPO.
As regards suspicious performances, when you see someone putting in amazing performances day after day, especially in the mountains or hilly territory, then you start the questions in earnest. Look at Sella in the 2008 Giro - two wins and a second in three days in the mountains. I can think of at least one other who managed to garner three successive mountain finish victories in a grand tour having previously managed a back-to-back first and second in the same kind of terrain the previous week. Did that happen much before 1990? I don't think so, but I can only imagine Merckx doing so, and even that is a stretch.