midi synth not in tune

I noticed while playing piano synths that the pitch was off. i used a tuner, and the C I was playing was reading as a B that was 12 cents flat. The tune setting is set at 440 hz, and the midi notes are reading correctly (C note reads as a C), but still the note is wrong. I went into logic X, and the pitch was correct, so its isolated to mainstage 3.