Is this boiler a condensing model? (ie fitted in the last year or so) if so, check the condense discharge trap & pipe is not blocked (white 21.5mm plastic pipe leaving the boiler to a drain etc), if this goes into a rainwater down pipe, check the downpipe isn't blocked. Had the last instance happen to me whilst I was commisioning a new boiler and it p*ssed it down and filled the boiler with rainwater.
Failing it being a condensing boiler, it could be a flue fault collecting rainwater but unlikely. The heat exchanger could be faulty and leaking (is the system sealed or open vented? If sealed have you got a pressure loss? Open vented have you heard the header tank filling or dows the ball valve drip continuosly?) Reasons for heat exchangers failing range from badly set up and flame inpingement to the heat exchanger. Undersized boiler for house leading to low return temps in the heat exchanger is a cause to.
If you keep gettin water in your burner, it will knacker it as you may know leading to bills of up to £400 to fix. Let me know what you got (boiler size - age, how many bedrooms ect) and i'll search the relms of my brains.
Ben
April 2008