The most suspicious part of Nadal's time off is that he had just been tested when he was defeated by Lukas Rosol, a match he thought he would win and if Nadal had won he, would not have been tested after.
Also, Nadal now claims that he was getting injections in his knee before the match. I presume cortisone (a steriod), which would explain a positive test for steroid use. If he was on a silent ban I think it absurd that his cover story for why he couldn't play is the same cover story for a false positive test.
Lets not also forget Nadal's connection to the infamous doping doctor who supplied many Spanish cyclists. I certainly think there is good reason to suspect Nadal was on a silent ban, but we may never know (or maybe in a decade he'll write a memoir about it.).