I have a similar problem with my chimney. The leaks only occur during periods of heavey rain. Because I have a wide chimney and quite a bit of roof area in front of it, I suspect that the water is pooling and getting under the shingles. Once water is under the shingles, it may be getting under the overlap in the flashing. I may try using a continuous piece of flashing in front of the chimney or building something to shed the water around the chimney.