First rule of LLW design. “Thou shall not use multi tapping headers” Sorry but they are a PIN. And if systems arent perfectly matched and flow rates set correctly will leave you wide open to parasitic flow across the ports.
First thing I’d be checking is flow rate of your primary pump, Vs flow rate of your secondaries.
Something is pulling that flow water across the header rather than it circulating around it, so boiler then is ramping up as it’s running on its thermistor readings to control the gas rate. If the heat is going around the system rather than round the header it’s going to take an awfully long time before the temps are coming back to the boiler hot enough to start the modulation process
Achieving hydraulic separation through well-designed low loss headers is key for efficient heating and cooling systems. David Palmer and Baxi Heating’s Ryan Kirkwood provide detailed design guidance, including a recommended system configuration
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