FWIW, one of the posters on a Saints board talked to someone in the know regarding NFL testing. From that conversation, it is pretty clear that Thomas tested positive. The tests are two fold. The first looks for a "class" of possible drugs, while the second test identifies the exact drug taken. The second test is so precise that it can even identify how the drug was taken....ingested, inhaled, etc. I believe that the medication that Thomas was taking would show up as a "false positive" on the first part of the test, it would not show up as false positive on the second part.
Looks like Thomas has earned this suspension. It is a shame, because I really thought highly of him. Hopefully, our back up will hold his own.