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I'm most familiar with eQUEST for this issue.

Sometimes you have to hard enter coil capacities as the autosize routine doesn't work correctly sometimes. This happens frequently/randomly on preheat coils often. To meet the heating load eQUEST has the preheat coil, reheat coil, and possibly a baseboard in many of my models. I think it uses all of these together rather than individually as intended. In other words, the preheat coil may be set for 55F, but may not achieve that instead relying on the zone devices to meet the load. This doesn't always work so hard entering capacities can be a solution. I've had to do this with DX cooling coils too.

Changing reset schedules to gradually heat up or cool down after a nighttime setback can help too if the temperature difference is large.

Hope that helps.