Perhaps BO thinks he's still in Indonesia or Kenya. How do Indonesians or Kenyans bow when greeting someone?
It doesn't matter. He's in Japan.
To consider an extreme example that some people might get, recall the scene in Dune where Stilgar spits as a sign of extreme respect.
Presidents are expected to respect local customs, or at least have some clue as to what they are.
Obama apparently, does not.