hi my boiler is not working ?

i have had this boiler fitted(vokera unica HE) for 2 years now and i always have to empty it of water every time it rain .The water is coming in through the flue to the out side and every time i empty it it will always work(it fills up with water past the breather pipe for the gas regulator valve)last night there was so much rain it started to really fill up and i had to put towels in it every half hour till it stoped raining about 5 hours later.Now the thing wont work at all when i switch ot on it comes on for about 30secs then the red light will come on indicating a problem and when i reset it it just does the same so anyone any ideas how i can fix it I HAD THE GAS MAN OUT YESTERDAY FOR A LEAK HE FIXED THAT then it started raining so help needed cause its freezing and the gas man NOT coming back for 2 days