Fireplaces, Heating Stoves, Flues and Chimneys - more on leaking chimney

We found where the water is coming from by systematically using a hose on different parts of roof, flashing then the brick. It turns out it is coming in where there are three holes in the mortar on the chimney side that faces the roof, above the flashing. Like I said before, we had this thing rebuilt two years ago so it is not where the old flashing was attached. My question is, these holes look like they were put there on purpose. They are about the size of a pencil. Is there any reason for them or can I go ahead and seal them up? The water getting inside these holes is dripping onto the top of the fireplace insert, and pools then drips down the front of the metal vents of the front of the fireplace in the house. Thanks for bearing with me. This is kind of hard to describe. Susan

These holes sound like they may have been old anchor holes for a tv antenna.
Seal them up, and that should solve your problem.
Good Luck!