Inconsistency in curve calculations

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First thing to mention is that when you are trying to match HVAC stuff, always request the Detailed (= HVAC System Timestep) frequency, not the Timestep one. You'll avoid many problems where you don't even realize that might be due to the fact that several HVAC timestep may happen within a single (Zone) Timestep.

In this specific case, it may not be a problem since I see the file has Timestep, 12;, but this is a rule you should always follow.

Second, there is a note in the I/O ref that is easy to be missed. Emphasis is mine below, quoting the I/O ref guide here:

Field: Cooling Capacity Function of Temperature Curve Name

The name of a biquadratic performance curve (ref: Performance Curves) that parameterizes the variation of the cooling capacity as a function of the leaving chilled water temperature and the entering condenser fluid temperature. The output of this curve is multiplied by the reference capacity to give the cooling capacity at specific temperature operating conditions (i.e., at temperatures different from the reference temperatures). The curve should have a value of 1.0 at the reference temperatures and flow rates specified above. The biquadratic curve should be valid for the range of water temperatures anticipated for the simulation.

Note: The curve is evaluated at the leaving chilled water (=evaporator outlet) setpoint temperature, not the actual leaving chilled water temperature.

So that's one thing to be aware of. As you can see in the graph below, that explains the discrepancy, and if you use the right variable, you'll get it right

Third, as far as the Condenser Inlet Temperature versus Performance Curve Input Variable 2 Value, I did find a small discrepancy... This might be explained by the fact that curve is evaluated early in the iteration cycle and the actual node temperature ends up slightly different or something, I am not sure and I don't have more time to spare on this.

For reference with the files you supplied, I changed the Output section at the end to be this:

! SENSORS
Output:Variable,*,Chiller Part Load Ratio,Detailed;
Output:Variable,*,Chiller Evaporator Outlet Temperature,Detailed;
Output:Variable,Main Chiller Cnd Inlet,System Node Temperature,Detailed;

Output:Variable,Chilled Water Loop ChW Pri Pump Outlet,System Node Temperature,Detailed; ! ChW Inlet
Output:Variable,Main Chiller ChW Outlet,System Node Temperature,Detailed; ! ChW Outlet
Output:Variable,Main Chiller Cnd Inlet,System Node Temperature,Detailed;  ! CndW Inlet
Output:Variable,Main Chiller Cnd Outlet,System Node Temperature,Detailed; ! CndW Outlet
Output:Variable,Chilled Water Loop ChW Pri Pump Outlet,System Node Setpoint Temperature,Detailed; ! ChW Inlet
Output:Variable,Main Chiller ChW Outlet,System Node Setpoint Temperature,Detailed; ! ChW Outlet
Output:Variable,Main Chiller Cnd Inlet,System Node Setpoint Temperature,Detailed;  ! CndW Inlet
Output:Variable,Main Chiller Cnd Outlet,System Node Setpoint Temperature,Detailed; ! CndW Outlet

! final Multipliers
Output:Variable,*,Chiller Capacity Temperature Modifier Multiplier,Detailed; !- HVAC Average []
Output:Variable,*,Chiller EIR Temperature Modifier Multiplier,Detailed ...