Funny, in those docs it tells you the 4th axis is available if the charge pump is turned off.. but doesnt tell you how to turn it off..
Anyway, if your sure the charge pump isnt happening, then probably best to troubleshoot that.
In darwin, there is a reset on the ports page to put darwin out of any estop it may be in... us that first
so that darwin is not in ready state,m if it wont come out of Estop, then check the Estop input isnt inverted
or something, Reset should work and turn the system green to go.
Next, check that charge pump, it should as you saw turn yellow if set to a frequency output, test it at 12.5Khz and also at 25Khz..
or a few others... some boards are very sensitive to frequency so maybe its pulsing too fast for it.. or too slow..
See if any of that gets the board to reset properly..
Art