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I stand corrected from my comment above. The AirLoopHVAC:UnitaryHeatPump:WaterToAir object can model cycling water-side flow rate. However, the model fails to account for this after the model sets the water flow rate and on subsequent iterations fails to set the water flow rate back up to design to model the coil. Might be TMI here, but that's what's happening.

In your input file, set the last input for Heat Pump Coil Water Flow Mode to Constant or ConstantOnDemand. Your AHUs don't have this input and it defaults to Cycling.

AirLoopHVAC:UnitaryHeatPump:WaterToAir,
  rtu2,                    !- Name
  availability_tbd,        !- Availability Schedule Name
  rtu2 Mixed Air Node,     !- Air Inlet Node Name
  rtu2 Air Loop Outlet Node,  !- Air Outlet Node Name
  0.94389,                 !- Supply Air Flow Rate {m3/s}
  Thermal Zone: Copy_Room, !- Controlling Zone or Thermostat Location
  Fan:OnOff,               !- Supply Air Fan Object Type
  rtu2 fan,                !- Supply Air Fan Name
  Coil:Heating:WaterToAirHeatPump:EquationFit,  !- Heating Coil Object Type
  rtu2 htg coil,           !- Heating Coil Name
  0.001,                   !- Heating Convergence
  Coil:Cooling:WaterToAirHeatPump:EquationFit,  !- Cooling Coil Object Type
  rtu2 clg coil,           !- Cooling Coil Name
  0.001,                   !- Cooling Convergence
  2.5,                     !- Maximum Cycling Rate {cycles/hr}
  60,                      !- Heat Pump Time Constant {s}
  0.01,                    !- Fraction of On-Cycle Power Use
  60,                      !- Heat Pump Fan Delay Time {s}
  Coil:Heating:Fuel,       !- Supplemental Heating Coil Object Type
  rtu2 supp htg coil,      !- Supplemental Heating Coil Name
  50,                      !- Maximum Supply Air Temperature from Supplemental Heater {C}
  21,                      !- Maximum Outdoor Dry-Bulb Temperature for Supplemental Heater Operation {C}
  rtu2 Outside Air Inlet Node,  !- Outdoor Dry-Bulb Temperature Sensor Node Name
  BlowThrough,             !- Fan Placement 
  always off;              !- Supply Air Fan Operating Mode Schedule Name

Add this to the end of this and other objects like this (and also change the semi-colon on the last input above to a comma):

  ,                 !- Dehumidification Control Type
  Constant;    !- Heat Pump Coil Water Flow Mode

VERY IMPORTANT....you must change always off; to always off,