If you are using the G540 connected to a PMDX-126 via the ribbon header J19, you do not need (and can not use) the G540's charge pump feature. As long as you have the charge pump enabled on the PMDX-126, the PMDX-126 will make sure that the step and direction signals to the G540 are held inactive (low) until there is a valid charge pump (and also no EStop). So disable the G540's charge pump.
The longer answer is that the "pin 16" signal on J19 comes from the 2nd parallel port on the PMDX-126, not from the the first parallel port. That allows 6 step/direction pairs of signals along with spindle control on port 1 pins 14 and 16, and charge pump on port 1 pin 17. This mode has 4 step/dir pairs coming from the first parallel port and 2 more from the 2nd parallel port. There *is* a mode on the PMDX-126 ("Jumbo" mode) that drives J19 pin 16 from parallel port 1, but that simply clones the signal from pin 3 (creating a hardware slave motor on pins 16/17 that is a copy of pins 2/3).
Bob