So it appears as though someone has tweaked the gain on the SCR's to try to compensate.
You can check the gain settings in the PIC Setup Screen to compare the 3 zones. It sounds like someone tried to optimize a difficult situation. Because heat rises, the bottom zone heats the other two, therefore to keep the temperatures close to the same, the bottom heater should have been much larger. If it is not, then it could be difficult to come up with a set of PID variables that will control at all points while ramping from ambient to process setpoint. However, creating PLC-controlled ramps in Manual Mode for each PID zone might help, by adding a way to achieve setpoint on each zone without overshooting. Once setpoint is reached, the PID is switched from Manual mode to Automatic mode.
For example, a timed ramp in PID Manual Mode is set up for each zone, with the bottom zone have a much steeper ramp, and the other two with progressively shallower linear setpoint ramps. This allows time for the bottom heat to rise and helps to prevent overshooting the two top zones. This only works where there is time to allow for a longer, slower heat-up. A simple ramp can be created with a timer. Say you determine that adding 1 degree every 1 seconds will work for the bottom, 1 degree every 2 seconds for Zone 2, and 1 degree every 3 seconds for the top zone. So you start all zones with a Setpoint = Current Temperature, then add degrees to each zone setpoint accordingly. The top zone will arrive at its setpoint much later, so there will be time for the bottom heat to rise and avoid overheating the top zones.
No time for heating ramps? You might have to live with what you got now. Using thermodynamic equations for heat transfer, and finding the heat transfer rate though each zone, and the amount of heat addded in each zone, theoretical equations could be derived that would allow adding only the necessary heat in each zone. Whether that is practical depends on how important it is to fine-tune this system.
This problem reminds me of the times I have spent the night on the 3rd floor in a hotel on a cold night. At first, the room is ice cold and you crank the thermostat up and set the heater to High. About 2 AM you wake up sweating. The heater is off and stays off. You remove the blanket and lie on the bed trying to get cool, but the room only gets hotter. The heat from the lower floors has arrived. Finally you turn the thermostat from HEAT to COOL and turn on the air conditioning.
If the top zone heat is turned off (PID CV Output = 0), that is all the PID can do for you once the top zone termperature is above setpoint. To prevent the overshoot, the bottom heater will have to be cut off earlier than its PID wants to shut it off, or you will have to add cooling!
Really the 3 zones are inter-acting, but the 3 separate PIDs are independent and have no knowledge of each other. To get better control, the 3 zones will have to be treated as a system, with heat from Zones 1 and 2 being transferred to Zone 3.