If I can make a controversial speculation about Nadal, it would be this -
He's scared of losing and his hurting his macho, no-one-beats-me-unless-I'm-injured image. How injured he was in 2012, only he knows. Certainly it wasn't like he succumbed to any obvious physical problem on the court unable to move another inch when losing to Rosol.
Nadal fans like to take the side of saying, "well, he played through heavy medication for pain relief". My question is, how do you know? It is just as likely that even if injured, that they weren't a factor as much as he makes them out to be.
Even now, if he says that the knees are well, then it seems premature to pullout of the AO because of a stomach bug. It seems he doesn't want another earlier round loss to an inspired opponent.