I think I've answered my own question. It appears that if the "A" samples are missing, i.e 069-A.wav etc, Hauptwerk takes the pitches of the closest samples, averages them, and calls that the "preferred" pitch for the organ. In my case I had no "A" samples at all, only G# samples. Evidently Hauptwerk took the average of those pitches and called it the organ base pitch. Hence it declared my base pitch as exactly a half step low or A=415.3Hz. When I generate and add "A" samples Hauptwerk calculates the base pitch correctly.
This really shouldn't be, but since it probably hasn't bothered anyone else, and I understand it now, I will not complain about it