It certainly seems that the samples from that day had been contaminated. Otherwise he would have been found out before.
They don't test for synthetic testosterone UNLESS the T/E ratio test shows that something is amiss. The situation would go something like this:
Rider X is on a doping schedule that includes testosterone, EPO, and other banned substances. The schedule includes masking agents that will allow the rider to test negative in any doping controls.
Rider X has a terrible ride in an alpine stage of a major stage race. Now seemingly out of contention, his team doctor gives him a new elixir that he says will help him recover. He also tells him that there is a masking agent to ensure a negative test.
Rider X takes the potion, wins the stage, and rises to win the overall race against what seemed like insurmountable odds! Except there is a problem...the masking agent didn't work correctly and Rider X has a T/E ratio that is off. The race officials decide to test the rider's sample further in order to confirm if there is an issue. After running a carbon to using EPO. He was banned for two years and just came back.