due to flashing coming out of the brick mortar of the chimney stack and other things. We have made wonderful stides in building homes, but have not perfected the marriage of the roof to the chimney stack.
I would NOT back off this home IF you like it because of this chimney/roof deal. Fix it and fix it with a reputable roofer COMPANY.
Chimneys, skylights, stacks, turbines and any other protrusion off the roof is very susceptable to leaks now or in the future.
once the roof/chimney is repaired, conduct periodical visual inspections of the flashing and the condition of the roof around the chimney. If the roof down slopes directly into the chimney, perhaps a "cricket" is needed to further divert the water "away" from that crucial intersection.
Remember, the word "reputable" in seeking a roofer. seek a company, not an independant contractor.