A picture is worth a thousand words, and I tend to make a lot of mistakes in my words, so, first picture, the circuit in question:
I know the Dickson charge pump looks a little different but it is essentially the same.
EDIT: We can basically forget about the charge pump type whether it is MOSFET or diode or if the MOSFETs are from drain-source, etc. The problem remains the same.
Below is my pulse engine which does a fantastic job of providing me with two sets of pulses - until I hook them up as in the next two pictures.
Picture 1. The pulses are not hooked up to the negative side of the capacitors and
Picture 2. The pulses are then attached and the pulses are not at all the way I want them, that is, they do not alternate and one of the two no longer returns to ground.
I've used op amps to create the pulses and inverted pulses and bipolars - but that's not really the problem. It's that there needs to be an outlet or something for the capacitors.
I've tried to put PNP transistors that fire when the alternating pulse drops to zero. I've used resistors and also a lot of other embarrassing things I won't talk about.
I've tried to put high pass or band pass filters on each pulse line but that does not work at all.
The question, again, is: How to keep the pulses alternating and returning to ground after connecting them to the negative half of the capacitors in a topology like this?