I would call back the roofer who put it on and tell him again, it is leaking. I would show him where it is leaking. I would have my contract out and sitting there and ask him, " now what are you going to do here?" Maybe, you could have someone with you who is experienced in this. I have an older neighbor I always use, I rent him by the hour for this stuff, lol.
To me it sounds like the flashing isn't bent right around the chimney. My roofer makes his own flashing and mine is bone dry. Maybe, some tar?