Keyboards and organs have to be tuned a little different than an acoustic piano. An acoustic piano is not perfectly in tune with itself when you take into consideration the fundamental and the upper harmonics. When a piano is tuned, the middle or temperment octave is set and then as you go up or down in octaves those notes are tuned to upper partials rather than to the fundamental. On top of that each piano is a little different.

On an arranger keyboard, essentially a portable organ, not only is the middle octave tuned with the same temperment, but the upper and lower octaves need to be tuned to the fundamental of the middle octave rather than upper partials. If you play a perfectly tuned piano with an organ or keyboard you will find out that they are not perfectly in tune with each other.

If you should want an acoustic piano to be tuned identically to an organ or keyboard then the piano will not sound quite natural.

This was explained to me by a professional piano tuner when I was a piano dealer.

This may be what you are hearing. The Yamaha keyboard is tuned perfectly with itself and not like a regular piano.

Now that I think of it, it may be that the electronic keyboards are slightly detuned as much as they can to make it sound as real as possible. But this is the general idea as explained to me.