If the fan does not run slowly when just the pilot is lit then the flame will suffocate, until enough oxygen has made it into the combustion chamber it is going to be difficult to re light.
When you turn on the electricity to the boiler with no CH/hot water demand you should hear the fan start slow running.
If you dont hear the fan, then a faulty microswitch, dry joint or open circuit slow run resistor may be causing the fan not to run and remove pilot flame combustion products.
fred
November 2007