I think Peter Bodo is asking the right questions. Whenever Nadal has a dramatic loss he seems to flee the ATP Tour. Remember 2009 when Nadal lost to Soderling his parents were also having marital problems and almost divorced. Nadal's parents have since gotten back together but his personal problems were more the reason he missed Wimbledon in 2009 despite being the defending champion.
Nadal probably had knee problems but I sense his problems are more personal and emotional. I doubt Nadal is going to tell the media the truth but I think something happened in his personal life and he probably had a crisis of self confidence too.