I have answered my own question. The accuracy improves the more FFT samples. Using the maximum samples (65536) the reported frequency is good. Usually within 0.2Hz, which is close enough for me.
I downloaded AUDio MEasurement System as I created a Top Octave Generator program for an Atmega328P running at 16MHz. The Atmega328P is required to produce 12 simultaneous square waves with frequencies between 3520Hz and 6645Hz. I had no way of testing if the program was producing anything. The System did the job, proved that it was producing the desired output. The reported frequencies were close (within 10Hz) but not exact. I don't think this is a problem, if the System reports frequencies that...