I wouldn't read too much into the fact that the positive sample was taken after stage 11, and not after one of the stages he won (or the TT). One common misconception is to think that when a test is negative, then the rider must be clean. Legally he (or she) is clean, of course. No doubt about it. But we've learned from cases like Armstrong, Rasmussen and many others that these riders could deliver negative tests time after time although they were still on all sorts of juice.
When a lab in 2004 made retro EPO testing of urine samples from the 1998 Tour they found two negative and one positive sample from Stuart O'Grady. When the results were published - duing the 2013 Tour - he admitted that he was on EPO in 1998 and announced his retirement. But notice that there were two negative samples (could have something to do with the samples spending 6 years in the lab, I don't know). If he'd only delivered the two negative samples - by chance or luck - then we'd all think he was a clean rider. But he wasn't! He was on EPO during the 1998 Tour. The labs only find what they're looking for, and they have to be pretty certain with a very low margin of errors.