Dip switches set for Auto startup, +43 seconds for feed amount (1,2,3 is on,off,on)
Does the unit feed pellets after the initial feed for startup? I am wondering if the ESP is not seeing a high enough number and shutting the unit down. A completely cold boiler will take more to get the ESP up to a certain temperature because of the water drawing that much heat off of the flame.
You could try setting your DIP switches to 1 - on, 2 - on, 3 - off to set +64 seconds for the "charge" cycle. You will have to watch and see how many pellets are actually being loaded into the firepot.