Sorry for being so vague. I mean turning off the voltage to the base. Band by turning off the voltage, I mean pressing the button on the Fixed Voltage component.
This only seems to happen when transistors are connected to each other and after clicking the voltage on and off a few times. For example, in the circuits posted above by Fizik_S clicking the voltage on and off a few times to the base of each PNP always gives the desired results. But on the circuit I posted, with the 5V and 2V on, for a few clicks of turning the 3V on and off it behaves as expected, but after a few clicks the probe stays stuck a certain voltage (not always the same) and it takes turning the 5V off and on again to clear it.