Dano, I had a similar problem on our house here in Florida. Agree with
another poster, if its a steep pitch, let a roofing guy get up there
and do it. No sense breaking your back to save a few bucks. My problem
turned out to be not the seal around the base of the chimney but nails
had come out of the flashing leaving small holes all the way through
the roof. If you house is like mine, like most new houses, it has
pressboard instead of plywood for the roof, according to the roofing
guy, nails used to hold down flashing don't hold as well in pressboard
and actually should be caulked over after being nailed in. Another nice
thing about letting a roofing guy do the job is that he can check other
areas of the roof while he's up there just to make sure everything is
ok.

regards, Phil