The original test may have been a simple hematocrit level test, but subsequently they looked for genetic markers showing that some of the blood cells came from someone else's bone marrow. His Olympic B sample had been frozen and so, by the lab's protocol, could not be used to confirm the A sample test. Without the confirmation he could not be sanctioned.
The later positive test from the Giro (was it the Giro?) was confirmed with the B sample.
It is simply incorrect to say that the test has an unknown rate of false positives. To the contrary, the test is very, very accurate. The test is so good that there are very few plausible or even possible alternate explanations for a positive result. One exlpanation, and by far the most likely, is that someone else's blood was injected. ANother explanation, and one which I frankly find rather hard to accept, is that lodged somewhere within TH's body are cells from a vanishing or chimerical twin that began forming in the womb with TH but whose body was absorbed by TH, while still in the womb. This means that the cells are technically from another person, hence the test results, but that they are not the result of cheating. The Chimerical Twin idea is explained here in a subscription required NYT article:
http://query.nytimes.com/gst/health/...6C0A 9639C8B63
I like TH a lot and have always admired him. Honestly, if he was doping then my guess is most of the riders are doping, including Armstrong, but I sure find his claim hard to swallow.