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You should verify how much load the HVAC system is delivering to each zone. Some good variables for this are:

Output:Variable,,Zone Air System Sensible Heating Energy,hourly; !- HVAC Sum [J] Output:Variable,,Zone Air System Sensible Cooling Energy,hourly; !- HVAC Sum [J] Output:Variable,,Zone Air System Sensible Heating Rate,hourly; !- HVAC Average [W] Output:Variable,,Zone Air System Sensible Cooling Rate,hourly; !- HVAC Average [W]

Verify what your control zone is by looking at the control zone name field. It is possible that the control zone is being well conditioned while the other "slave" zones are not being conditioned. You mentioned you want to control 2 different zones. It is possible that the control zone is being conditioned while the other zone is not. Are the mean air temperatures for both zones not behaving?

https://bigladdersoftware.com/epx/docs/9-5/input-output-reference/group-unitary-equipment.html#field-controlling-zone-or-thermostat-location-1

You should also examine the Unitary:HeatCool objects Availability Schedule; make sure the schedule values are not 0 when they should not be, as this would indicate that the system is forced off for that timestep, and cannot come on to condition your zone.

https://bigladdersoftware.com/epx/docs/9-5/input-output-reference/group-unitary-equipment.html#field-availability-schedule-name-1-012

"correct specification of the heat/cool furnace requires specification of the following objects in addition to the furnace object:"

-list of objects

I would look at the inputs for the below two component objects especially, particularly looking at the Rated Air Flow Rate, the rated capacities (Gross Rated Total Cooling Capacity for dx cooling coil and Nominal Capacity for furnace/burner), and the Capacity Function of Temperature curve object for the dx cooling coil.

cooling coil (Coil:Cooling:DX:SingleSpeed) https://bigladdersoftware.com/epx/docs/9-5/input-output-reference/group-heating-and-cooling-coils.html#coilcoolingdxsinglespeed

heating coil (Coil:Heating:Fuel) https://bigladdersoftware.com/epx/docs/9-5/input-output-reference/group-heating-and-cooling-coils.html#coilheatinggas-000

Similarly to the Unitary:HeatCool object's Availability Schedule, I would check to ensure the Availability Schedules of the individual Coil:Heating:Fuel and Coil:Cooling:DX:SingleSpeed are not 0 when they should not be.

https://bigladdersoftware.com/epx/docs/9-5/input-output-reference/group-heating-and-cooling-coils.html#field-availability-schedule-name-4-003

https://bigladdersoftware.com/epx/docs/9-5/input-output-reference/group-heating-and-cooling-coils.html#field-availability-schedule-name-6-001

https://bigladdersoftware.com/epx/docs/9-5/input-output-reference/group-heating-and-cooling-coils.html#field-total-cooling-capacity-function-of-temperature-curve-name

https://bigladdersoftware.com/epx/docs/9-5/input-output-reference/group-heating-and-cooling-coils.html#field-total-cooling-capacity-function-of-flow-fraction-curve-name

"The output of this curve is multiplied by the gross rated total cooling capacity and the total cooling capacity modifier curve (function of temperature) to give the gross total cooling capacity at the specific temperature and air flow conditions at which the coil is operating."

If the rated capacities and rated airflow rates are too small, that may be causing under conditioning of your zone. If the capacity function of temperature curve object coefficient inputs (for the DX Cooling Coil) are "bad," that can result in very low actual cooling capacity during the course of the simulation.