Is it the one with diodes and caps? If that's the case, the voltage stored in every stage loses the voltage drop over the diode from the previous stage..
so you get (n+1)vdd - nvD where vD is the diode ON voltage drop.
because of the threshould voltage of the switch, vout!=(n+1)vdd. Since the vth increase with the stage increasing, vout does not increase proportionally
I'm presuming that all the transistors are NMOS transistors (since you said bulk is connected to ground).
The transistors that are connected to a high voltage (that's about 2/3 of your switches) should be PMOS, with bulk to VDD. An NMOS has a limit on conducting a high voltage.