I finally got around to attempting to program the ProgRock today and I seem to have the same issue as described in the first post in this thread by Ian G4JQT. I am also using rev 1.02. The manual (for v1.02) does state that the LED will flash 4 times after each button press in section 2.4. But I find that more often than not, the LED flashes once. If I keep hitting the button, 2,3,4 times or more, I will eventually get 4 flashes. But as yet, I haven't been able to program any desired frequency. If I leave all the switches in the on position, not a valid configuration I realise, I do get 27,0031MHz on Clk0/1. Then 210kHz on Clk2. I did try to program the ProgRock ignoring the number of acknowledgement flashes but that didn't work either.

From the ProgRock operating manual. Pr1.02

"You setup a digit on the 4-way DIP switch then press the button briefly. The LED flashes 4 times quickly to confirm the button press. Wait for the LED to stop flashing. Then setup the next digit."

The default build was used with the LM317LZ mounted on the ProgRock board. Voltages are good on the test points. 5.2V and 3.1V. I am using a regulated 9V supply.