Check the controller to controller group wiring.. there's typically a SOM, switch over module in each controller, which allows controllers to apply power to the group functions, bypassing units and pulling power from others as units loose mainline power or are shut down. There are basically two groups of wires, power and comm, going from 1-2, 2-3, 3-1, creating a loop.
If all that looks good, check the tool and ensure that each controller is labeled correctly ie; 1, 2 or 3. Ensure all code / function settings are same in each controller regarding ocs and group
