I have a couple theories. First, as Rick D. alluded to, when testing this, make sure that keyboard split and auto accompaniment are both switched off. Having either one of these features on can put an entirely different sound, other than the main voice that you have selected, on the lower part of the keyboard.
With that said, none of these features should cause any of the notes to sound a fifth (or an octave and a fifth) above the key you are playing, as in you say you are playing an F, but hearing a C. And, while the E463 has functions to allow you to change the octave of the sound you're playing, it does not have a function to independently tune specific sounds or specific parts of the keyboard to non-octave intervals in relation to other sections of the keyboard. In other words, even if you have split voice, auto accompaniment, or even dual voice on, there is nothing on this keyboard that allows those sections to be tuned a fifth above the main voice -- you can only select octaves. The keyboard does have a transpose feature, but that affects the entire keyboard at once, and would not cause part of the keyboard to play at a different interval than another part.
So, what I think what is happening is related to the fact that this is occurring on an organ sound. Many organ sounds are made up of flute or sine-wave type sounds that are tuned to intervals, and these intervals can, indeed, be a fifth above the main note being played. In the realm of a drawbar organ, like a traditional Hammond, drawbars labeled as 5 1/3', 2 2/3' and 1 1/3' all produce a tone that is a fifth above the main note being played. The lower the number, the higher the octave, so that an organ sound can consist of tones that are an octave and a fifth apart.
Therefore, what may be happening is that the organ sound you are playing (the '60's organ sound you mentioned) may consist of components that are a fifth, or an octave and a fifth, above the main note (while the E463 cannot independently tune sounds to an interval like that, the preset sounds themselves can easily be made up of samples that include these intervals). So, when you play the low notes of the keyboard, the speakers may not be as capable of playing the deeper bass sounds of the main note of the key you are playing, and the component of the tone that is an octave and a fifth above the main note could be more prominent, making it sound like you are hearing a C when you are actually playing an F.