Potterton Suprima 40 - leaking flue?

I thought the boiler was leaking so called an engineer, he checked it and it's working fine. It was strange as the water was on top of the boiler as well as on the floor. It now appears that this happens only when it rains - it appears water is coming in the flue and seeping out where the pipe joins the top of the boiler. Can anyone suggest how I can stop this from happening.

Thanks