Do you have a picture of your existing chimney/roof installation? Generally, the modified bituminous roofing membrane (or any other "flat roof" membrane), needs to extend up the adjacent vertical surface about 200 mm (8"). It shouldn't just stop where the flat roof meets the vertical surface, in this case the chimney. If you post a picture of your installation, I can offer some advice as to how the counter flashing, roof membrane, etc., should be installed.
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