Thanks so much buildersmate, I'm going to try it this weekend.
I've tried to find pics of the kind of flashing I mean but can't find any! Should really take one myself.
It kind of looks like 17 on this pic...
http://www.a-lineroofing.com/roofingterms.ivnu
...but it's not a chimney but a 12 inch high dividing wall between my pitched roof and the neighbours'.
I can see a gap between the flashing and the brick wall, just like it's come away, about half inch. Enough to let rain in though isn't it?!
I'll try the caulk then if all else fails just whack a bit of tape on it and see if that helps!
Thanks