You do not say the make or model of your boiler...
The pilot flame has a heat sensor that sends a signal to the control board - the flame may be too weak to trigger a sufficient signal - the sensor itself may be defective - the control board may not be responding to the correct signal. The control board may be failing to tell the gas valve to open or the gas valve may be defective and not opening when told to do so.
A certified engineer should be able to diagnose which it is - a sensible engineer will begin by looking for the signal to open the gas valve.
Peccavi
November 2010