According to his daughter Karen, in this interview
of 1999, it was her understanding that the little snippets of FJ's work which were included in the first three films were done by production staff who happened to enjoy his contributions and technical work. He was never given any formal credit for those elements, and his decision to not accept the opportunities as a creative consultant could have arguably hurt him since it allowed Gene and Paramount to dismiss his work later as being "non-canon" stuff.
I found it extremely interesting to learn that she was shaking with rage during her first viewing of TMP. If I ever see that one again, I'm going to be very keen to catch the Tech Manual references if possible.