rhodies1,
I climbed up onto roof yesterday to take a look at things. Overall, didn't see any issue with the new roof seams at cap/roof mating area. Did see tho where the factory chaulking where sidewall and cap meet and the (correct name escapes me) plastic trim wasn't 100% so it could be possible that water was getting in there then running down inside it and coming out at pinbox. (???).
On a side note, the roof was installed in early July and have to say it was still clean as a whistle (except where I just walked across it w/ dirty sneaks) and don't see any black streaks!!! I'm happy!!!!