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Autosizing can be problematic for any component in eQUEST, but it appears to be problematic randomly.

I've had to hard enter capacities for chillers, boilers, and preheat coils in the past to get them to work properly.

It's important to look at the hourly reports to confirm set point temperatures are being met for every hour.

If you're early in the design, you can use ASHRAE 90.1 guidance and over size your chiller by 15%, and your boiler by 25% to have a realistic capacity.

Good luck.