I have very often problems with setpoint temperatures. The reasons are a lot: among the output variables check system node temperatures and system node flows, heating rates, sizing parameters, if in Sizing:System the "Type of Load to Size on" is "sensible", the properties of the envelope, natural ventilation...
Are you modeling AHUs that supply many zones?
Are you modeling radiant floors or ceilings?
With those systems I have often problems. Check how the system is controlled, check the position of the internal source...
Best Regards