From the initial complete rework forward had numerous leaking problems that ruined two kitchen ceilings that adjoined the chimney and fireplace (the fireplace-chimney is in the kitchen). Part of the problem was due to the fact Beere and Sons (i.e., their employee) simply don't know how to properly flash a chimney.
When the leaking occurred after rains and was even worse than it had been prior to their work (especially rains when the wind blew from the north; it seemed as though straight down rains more often than not didn't result in leakage problems) they told me the chimney was the problem; the bricks needed sealed, and it was a big chimney (9' long) and all big chimneys leaked! I sealed the bricks, and continually kept caulking and recaulking - but the water kept coming in and ruined another ceiling (chalk the first ceiling up to Mr. Long).
On the last trip out several months ago the Beere installer tore up the edge of the flashing and ran a thick bead of silicone caulk along beneath it; he seemed surprised when he found the roofing nails in the flashing were rusted, as he couldn't fathom that his install job was at fault.
They used 4 pieces of scrap aluminum - with overlaps on the back of the chimney; said couldn't get a piece 9' long. At every jointure there seemed to be a leak. Moreover, the flashing was nailed and caulked (i.e., partially caulked; the job wasn't continuous) on top of the shingles, whereas several other roofers who looked at it said it should have been under the shingles.
Regardless, as previously stated Mr. Beere blamed the leak on the size of the chimney, new bricks not being sealed and absorbing water, everything but the facts he really didn't know how to install flashing on the back side, had cut about 1/8" groove into the bricks (too shallow; I was told by others should have been 3/4-1" deep into the mortar joint, not the bricks), had used too narrow pieces of flashing (i.e., had used scrap lying around rather than quality metal (i.e., one piece which was wide enough and long enough)), hadn't caulked continuously (even though he ripped the metal up on the most recent attempt to correct the leaking problem, recaulked, and renailed - he still left gaps w/o caulking (the gaps were evident when we tore his flashing job out on 6/3/13, as was the fact the entire length of the roof sheathing underneath his flashing job was still soaking wet), and had put the bottom side of the flashing on top of the shingles - rather than under them. This proved to be an expensive nightmare, due to ceiling damage, the Beere attitude it was the chimney's fault, reluctance to use other than scrap metal, and bad flashing mechanics/know-how (e.g., flashing on top of shingles and not underneath).
On 6/4/13 I had an older man (Gary Ritter) reflash the back side of the chimney and install ice guard. He laughed when he saw the flashing on top of the shingles - as did several other chimney people who were called in to give estimates (they immediately said that was the problem). After two days of rain on 6/3-4/13 - the new flashing job by Mr. Ritter has held; there is no water on the ceiling and the chimney face isn't weeping - all of which goes to confirm: Beeres are incompetent in flashing chimneys, and all big chimneys don't leak.
However, in my estimation the Beeres are excellent roofers/shinglers, but this evaluation is not for the roofing repair job they did for us in early 2010.
Bottom line: don't let Beere and Sons touch your chimney - as they simply aren't up to snuff on proper flashing techniques all-around, and making statements such as all large chimneys leak, and the fact your bricks weren't sealed well enough - indicates that they've more likely than not consistently had problems with chimney flashing jobs they've performed (especially larger ones) - which they blamed on everyone (including the chimneys) except themselves!
In summary: I would hire Beere and Sons again to do roofing work - but I wouldn't let them near our chimney with a 50 ft pole!