I have an Apollo 80 and if the pilot-jet flame is not long enough to fully heat the thermocouple it shuts down the main burner when the water temperature thermostat shuts off the gas to the main burner. The main flame airflow "pulls" heat away from the thermocouple. If you have the drawing in the handbook it shows you where the adjustment is for the gas to the pilot jet. But check you haven't dislodged some crap into the pilot burner when you worked on the boiler, or knocked it slightly away from the thermocouple tip.
BryanL
February 2009